Starting phenix.real_space_refine on Thu Mar 14 22:32:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vmr_32036/03_2024/7vmr_32036.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 720 5.16 5 C 78192 2.51 5 N 21544 2.21 5 O 23088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 711": "OE1" <-> "OE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1733": "OE1" <-> "OE2" Residue "A GLU 1838": "OE1" <-> "OE2" Residue "A ASP 2001": "OD1" <-> "OD2" Residue "A GLU 2063": "OE1" <-> "OE2" Residue "A TYR 2091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2172": "OE1" <-> "OE2" Residue "A ARG 2358": "NH1" <-> "NH2" Residue "A PHE 2459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3692": "OD1" <-> "OD2" Residue "A PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3972": "OD1" <-> "OD2" Residue "A PHE 4509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4568": "OE1" <-> "OE2" Residue "A PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4905": "OE1" <-> "OE2" Residue "A GLU 4931": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 711": "OE1" <-> "OE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1733": "OE1" <-> "OE2" Residue "B GLU 1838": "OE1" <-> "OE2" Residue "B ASP 2001": "OD1" <-> "OD2" Residue "B GLU 2063": "OE1" <-> "OE2" Residue "B TYR 2091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2172": "OE1" <-> "OE2" Residue "B ARG 2358": "NH1" <-> "NH2" Residue "B PHE 2459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3692": "OD1" <-> "OD2" Residue "B PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3972": "OD1" <-> "OD2" Residue "B PHE 4509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4568": "OE1" <-> "OE2" Residue "B PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4905": "OE1" <-> "OE2" Residue "B GLU 4931": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 711": "OE1" <-> "OE2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1733": "OE1" <-> "OE2" Residue "C GLU 1838": "OE1" <-> "OE2" Residue "C ASP 2001": "OD1" <-> "OD2" Residue "C GLU 2063": "OE1" <-> "OE2" Residue "C TYR 2091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2172": "OE1" <-> "OE2" Residue "C ARG 2358": "NH1" <-> "NH2" Residue "C PHE 2459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3692": "OD1" <-> "OD2" Residue "C PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3972": "OD1" <-> "OD2" Residue "C PHE 4509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4568": "OE1" <-> "OE2" Residue "C PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4905": "OE1" <-> "OE2" Residue "C GLU 4931": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 581": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 711": "OE1" <-> "OE2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1733": "OE1" <-> "OE2" Residue "D GLU 1838": "OE1" <-> "OE2" Residue "D ASP 2001": "OD1" <-> "OD2" Residue "D GLU 2063": "OE1" <-> "OE2" Residue "D TYR 2091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2172": "OE1" <-> "OE2" Residue "D ARG 2358": "NH1" <-> "NH2" Residue "D PHE 2459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3692": "OD1" <-> "OD2" Residue "D PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3972": "OD1" <-> "OD2" Residue "D PHE 4509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4568": "OE1" <-> "OE2" Residue "D PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4905": "OE1" <-> "OE2" Residue "D GLU 4931": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 123548 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "I" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29421 SG CYS A4887 203.130 192.035 119.260 1.00 5.71 S ATOM 29446 SG CYS A4890 201.113 193.223 116.188 1.00 8.28 S ATOM 60307 SG CYS B4887 179.879 203.353 119.237 1.00 39.95 S ATOM 60332 SG CYS B4890 178.693 201.340 116.162 1.00 14.68 S ATOM 91193 SG CYS C4887 168.707 179.644 119.354 1.00 39.95 S ATOM 91218 SG CYS C4890 170.736 178.455 116.291 1.00 10.98 S ATOM A0H1B SG CYS D4887 192.032 168.532 119.373 1.00 39.95 S ATOM A0H20 SG CYS D4890 193.212 170.546 116.296 1.00 7.53 S Time building chain proxies: 44.82, per 1000 atoms: 0.36 Number of scatterers: 123548 At special positions: 0 Unit cell: (373.168, 373.168, 207.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 720 16.00 O 23088 8.00 N 21544 7.00 C 78192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.99 Conformation dependent library (CDL) restraints added in 13.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4890 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4887 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4890 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4887 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4890 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4887 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4890 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4887 " Number of angles added : 8 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31448 Finding SS restraints... Secondary structure from input PDB file: 664 helices and 104 sheets defined 69.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.56 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.501A pdb=" N VAL A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 270 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.998A pdb=" N LYS A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 322 " --> pdb=" O LYS A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 322' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.623A pdb=" N ARG A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.715A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.568A pdb=" N GLU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.624A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 541 removed outlier: 4.744A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.902A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 562 through 565 removed outlier: 4.377A pdb=" N LEU A 565 " --> pdb=" O LEU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 567 through 582 removed outlier: 4.102A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.128A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 588' Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.983A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.953A pdb=" N LEU A 637 " --> pdb=" O CYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.702A pdb=" N GLY A 809 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 878 through 901 removed outlier: 3.911A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.897A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN A 932 " --> pdb=" O GLU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1012 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.105A pdb=" N VAL A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.757A pdb=" N ASN A1046 " --> pdb=" O THR A1042 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA A1053 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1643 through 1647 removed outlier: 3.560A pdb=" N THR A1646 " --> pdb=" O LEU A1643 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A1647 " --> pdb=" O GLU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1643 through 1647' Processing helix chain 'A' and resid 1648 through 1665 Processing helix chain 'A' and resid 1671 through 1681 removed outlier: 3.857A pdb=" N SER A1679 " --> pdb=" O HIS A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1692 removed outlier: 4.366A pdb=" N LEU A1687 " --> pdb=" O GLU A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1711 removed outlier: 3.547A pdb=" N HIS A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1722 removed outlier: 3.533A pdb=" N MET A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1737 removed outlier: 3.743A pdb=" N ILE A1737 " --> pdb=" O THR A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.658A pdb=" N LEU A1788 " --> pdb=" O PRO A1784 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A1805 " --> pdb=" O LYS A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1833 Proline residue: A1821 - end of helix removed outlier: 3.664A pdb=" N GLY A1833 " --> pdb=" O LEU A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1848 removed outlier: 3.611A pdb=" N ILE A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1949 removed outlier: 3.571A pdb=" N GLN A1916 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A1930 " --> pdb=" O ALA A1926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A1937 " --> pdb=" O ALA A1933 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A1938 " --> pdb=" O LYS A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1965 removed outlier: 4.659A pdb=" N ARG A1962 " --> pdb=" O ALA A1958 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A1963 " --> pdb=" O ARG A1959 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A1964 " --> pdb=" O LYS A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1976 Processing helix chain 'A' and resid 1989 through 2006 removed outlier: 3.968A pdb=" N ASP A1993 " --> pdb=" O GLU A1989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2072 removed outlier: 3.690A pdb=" N VAL A2066 " --> pdb=" O SER A2062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A2069 " --> pdb=" O MET A2065 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2093 removed outlier: 3.852A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2101 removed outlier: 3.907A pdb=" N LEU A2097 " --> pdb=" O GLY A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2130 Processing helix chain 'A' and resid 2134 through 2151 Processing helix chain 'A' and resid 2152 through 2157 removed outlier: 3.818A pdb=" N GLN A2156 " --> pdb=" O LYS A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2165 removed outlier: 3.633A pdb=" N MET A2161 " --> pdb=" O HIS A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2179 removed outlier: 4.236A pdb=" N ASN A2176 " --> pdb=" O GLU A2172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2188 through 2205 Processing helix chain 'A' and resid 2208 through 2223 removed outlier: 3.744A pdb=" N ASP A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS A2216 " --> pdb=" O ALA A2212 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A2218 " --> pdb=" O PHE A2214 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR A2219 " --> pdb=" O ASP A2215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A2222 " --> pdb=" O SER A2218 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A2223 " --> pdb=" O TYR A2219 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2247 Processing helix chain 'A' and resid 2249 through 2256 Processing helix chain 'A' and resid 2260 through 2274 Processing helix chain 'A' and resid 2276 through 2283 Processing helix chain 'A' and resid 2292 through 2305 Processing helix chain 'A' and resid 2312 through 2326 Processing helix chain 'A' and resid 2327 through 2330 Processing helix chain 'A' and resid 2341 through 2355 Processing helix chain 'A' and resid 2356 through 2359 removed outlier: 3.825A pdb=" N ASP A2359 " --> pdb=" O PRO A2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2356 through 2359' Processing helix chain 'A' and resid 2382 through 2401 Processing helix chain 'A' and resid 2413 through 2426 Processing helix chain 'A' and resid 2427 through 2436 Processing helix chain 'A' and resid 2462 through 2475 removed outlier: 3.937A pdb=" N ALA A2466 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2491 Processing helix chain 'A' and resid 2491 through 2500 Processing helix chain 'A' and resid 2507 through 2524 removed outlier: 3.798A pdb=" N UNK A2511 " --> pdb=" O SER A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2547 Processing helix chain 'A' and resid 2553 through 2571 Processing helix chain 'A' and resid 2575 through 2589 Processing helix chain 'A' and resid 2594 through 2612 Processing helix chain 'A' and resid 2617 through 2635 removed outlier: 3.513A pdb=" N UNK A2621 " --> pdb=" O UNK A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2641 through 2649 removed outlier: 3.923A pdb=" N UNK A2645 " --> pdb=" O UNK A2641 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNK A2646 " --> pdb=" O UNK A2642 " (cutoff:3.500A) Processing helix chain 'A' and resid 2650 through 2657 Processing helix chain 'A' and resid 2713 through 2739 removed outlier: 4.085A pdb=" N ASN A2721 " --> pdb=" O GLU A2717 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A2722 " --> pdb=" O TYR A2718 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2769 removed outlier: 3.938A pdb=" N GLU A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) Processing helix chain 'A' and resid 2772 through 2784 removed outlier: 4.235A pdb=" N GLU A2776 " --> pdb=" O TRP A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2836 through 2863 Processing helix chain 'A' and resid 2877 through 2898 removed outlier: 3.787A pdb=" N ASP A2884 " --> pdb=" O GLU A2880 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A2887 " --> pdb=" O LYS A2883 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A2894 " --> pdb=" O ASP A2890 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A2895 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2941 Processing helix chain 'A' and resid 2962 through 2982 removed outlier: 4.350A pdb=" N UNK A2975 " --> pdb=" O UNK A2971 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N UNK A2976 " --> pdb=" O UNK A2972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3007 Processing helix chain 'A' and resid 3015 through 3029 Processing helix chain 'A' and resid 3105 through 3129 removed outlier: 3.775A pdb=" N UNK A3120 " --> pdb=" O UNK A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3137 through 3157 removed outlier: 4.213A pdb=" N UNK A3156 " --> pdb=" O UNK A3152 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK A3157 " --> pdb=" O UNK A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3163 through 3182 Processing helix chain 'A' and resid 3183 through 3200 removed outlier: 3.627A pdb=" N UNK A3187 " --> pdb=" O UNK A3183 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3220 removed outlier: 3.689A pdb=" N UNK A3219 " --> pdb=" O UNK A3215 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3251 Processing helix chain 'A' and resid 3255 through 3270 Processing helix chain 'A' and resid 3271 through 3277 Processing helix chain 'A' and resid 3281 through 3296 removed outlier: 4.123A pdb=" N UNK A3285 " --> pdb=" O UNK A3281 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3315 Processing helix chain 'A' and resid 3324 through 3356 Processing helix chain 'A' and resid 3362 through 3388 removed outlier: 4.132A pdb=" N UNK A3383 " --> pdb=" O UNK A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3391 No H-bonds generated for 'chain 'A' and resid 3389 through 3391' Processing helix chain 'A' and resid 3400 through 3420 removed outlier: 4.158A pdb=" N UNK A3404 " --> pdb=" O UNK A3400 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3434 removed outlier: 4.517A pdb=" N UNK A3428 " --> pdb=" O UNK A3424 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK A3429 " --> pdb=" O UNK A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3478 through 3496 removed outlier: 4.275A pdb=" N UNK A3495 " --> pdb=" O UNK A3491 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK A3496 " --> pdb=" O UNK A3492 " (cutoff:3.500A) Processing helix chain 'A' and resid 3503 through 3514 Processing helix chain 'A' and resid 3516 through 3527 removed outlier: 3.853A pdb=" N UNK A3527 " --> pdb=" O UNK A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3541 through 3548 removed outlier: 4.138A pdb=" N UNK A3545 " --> pdb=" O UNK A3541 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3579 Processing helix chain 'A' and resid 3612 through 3627 removed outlier: 3.823A pdb=" N VAL A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3644 Processing helix chain 'A' and resid 3661 through 3676 Processing helix chain 'A' and resid 3684 through 3698 removed outlier: 3.513A pdb=" N ASP A3692 " --> pdb=" O MET A3688 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A3698 " --> pdb=" O MET A3694 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3732 removed outlier: 3.768A pdb=" N GLU A3719 " --> pdb=" O GLU A3715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A3730 " --> pdb=" O GLN A3726 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A3732 " --> pdb=" O ALA A3728 " (cutoff:3.500A) Processing helix chain 'A' and resid 3734 through 3745 removed outlier: 3.554A pdb=" N LEU A3740 " --> pdb=" O ALA A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3766 removed outlier: 3.575A pdb=" N LYS A3759 " --> pdb=" O ALA A3755 " (cutoff:3.500A) Processing helix chain 'A' and resid 3769 through 3783 Processing helix chain 'A' and resid 3788 through 3797 Processing helix chain 'A' and resid 3803 through 3817 Processing helix chain 'A' and resid 3824 through 3828 Processing helix chain 'A' and resid 3831 through 3847 removed outlier: 3.699A pdb=" N CYS A3846 " --> pdb=" O LEU A3842 " (cutoff:3.500A) Processing helix chain 'A' and resid 3850 through 3859 Processing helix chain 'A' and resid 3868 through 3891 removed outlier: 3.718A pdb=" N TYR A3891 " --> pdb=" O PHE A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3923 removed outlier: 4.184A pdb=" N PHE A3905 " --> pdb=" O GLY A3901 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A3908 " --> pdb=" O ASN A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 Processing helix chain 'A' and resid 3938 through 3959 removed outlier: 3.599A pdb=" N HIS A3952 " --> pdb=" O HIS A3948 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A3955 " --> pdb=" O ALA A3951 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A3959 " --> pdb=" O MET A3955 " (cutoff:3.500A) Processing helix chain 'A' and resid 3963 through 3984 Processing helix chain 'A' and resid 3992 through 4005 removed outlier: 3.513A pdb=" N LYS A3996 " --> pdb=" O GLY A3992 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4021 Processing helix chain 'A' and resid 4022 through 4027 removed outlier: 3.804A pdb=" N SER A4027 " --> pdb=" O LYS A4023 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4035 removed outlier: 4.519A pdb=" N ASP A4035 " --> pdb=" O PHE A4031 " (cutoff:3.500A) Processing helix chain 'A' and resid 4044 through 4054 removed outlier: 3.728A pdb=" N HIS A4048 " --> pdb=" O LYS A4044 " (cutoff:3.500A) Processing helix chain 'A' and resid 4058 through 4069 Processing helix chain 'A' and resid 4078 through 4087 Processing helix chain 'A' and resid 4087 through 4108 Processing helix chain 'A' and resid 4111 through 4126 removed outlier: 3.727A pdb=" N PHE A4117 " --> pdb=" O ARG A4113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A4120 " --> pdb=" O THR A4116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER A4123 " --> pdb=" O GLU A4119 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL A4124 " --> pdb=" O LEU A4120 " (cutoff:3.500A) Processing helix chain 'A' and resid 4128 through 4130 No H-bonds generated for 'chain 'A' and resid 4128 through 4130' Processing helix chain 'A' and resid 4152 through 4160 removed outlier: 3.612A pdb=" N GLU A4160 " --> pdb=" O ARG A4156 " (cutoff:3.500A) Processing helix chain 'A' and resid 4161 through 4178 removed outlier: 3.757A pdb=" N GLU A4178 " --> pdb=" O ASP A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4183 through 4204 Processing helix chain 'A' and resid 4276 through 4285 removed outlier: 3.996A pdb=" N LEU A4280 " --> pdb=" O LYS A4276 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A4285 " --> pdb=" O ALA A4281 " (cutoff:3.500A) Processing helix chain 'A' and resid 4286 through 4302 removed outlier: 3.714A pdb=" N THR A4292 " --> pdb=" O SER A4288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A4300 " --> pdb=" O PHE A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4304 through 4309 Processing helix chain 'A' and resid 4479 through 4496 removed outlier: 3.811A pdb=" N TYR A4485 " --> pdb=" O LYS A4481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A4488 " --> pdb=" O ALA A4484 " (cutoff:3.500A) Processing helix chain 'A' and resid 4496 through 4515 Processing helix chain 'A' and resid 4567 through 4593 removed outlier: 3.862A pdb=" N ARG A4572 " --> pdb=" O GLU A4568 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A4590 " --> pdb=" O ILE A4586 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A4591 " --> pdb=" O ILE A4587 " (cutoff:3.500A) Processing helix chain 'A' and resid 4593 through 4613 Processing helix chain 'A' and resid 4613 through 4618 Processing helix chain 'A' and resid 4624 through 4630 removed outlier: 3.957A pdb=" N GLN A4628 " --> pdb=" O ASP A4624 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4661 through 4670 removed outlier: 4.224A pdb=" N SER A4666 " --> pdb=" O ARG A4662 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A4668 " --> pdb=" O ARG A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4671 through 4682 Processing helix chain 'A' and resid 4702 through 4715 Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 3.756A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4742 Processing helix chain 'A' and resid 4743 through 4748 Processing helix chain 'A' and resid 4749 through 4751 No H-bonds generated for 'chain 'A' and resid 4749 through 4751' Processing helix chain 'A' and resid 4752 through 4761 removed outlier: 4.257A pdb=" N SER A4758 " --> pdb=" O THR A4754 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A4759 " --> pdb=" O ILE A4755 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4807 through 4819 Processing helix chain 'A' and resid 4838 through 4854 removed outlier: 3.522A pdb=" N ILE A4854 " --> pdb=" O PHE A4850 " (cutoff:3.500A) Processing helix chain 'A' and resid 4857 through 4886 removed outlier: 3.741A pdb=" N ILE A4861 " --> pdb=" O LEU A4857 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A4869 " --> pdb=" O ILE A4865 " (cutoff:3.500A) Processing helix chain 'A' and resid 4893 through 4898 removed outlier: 3.942A pdb=" N PHE A4897 " --> pdb=" O GLY A4893 " (cutoff:3.500A) Processing helix chain 'A' and resid 4902 through 4910 Processing helix chain 'A' and resid 4913 through 4928 removed outlier: 4.477A pdb=" N ASP A4928 " --> pdb=" O LEU A4924 " (cutoff:3.500A) Processing helix chain 'A' and resid 4933 through 4946 Processing helix chain 'A' and resid 4956 through 4961 Processing helix chain 'G' and resid 57 through 66 Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.501A pdb=" N VAL B 269 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 270 " --> pdb=" O VAL B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.999A pdb=" N LYS B 321 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 322 " --> pdb=" O LYS B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.624A pdb=" N ARG B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.715A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 463 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.568A pdb=" N GLU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.624A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 541 removed outlier: 4.743A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.902A pdb=" N CYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 562 through 565 removed outlier: 4.377A pdb=" N LEU B 565 " --> pdb=" O LEU B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 565' Processing helix chain 'B' and resid 567 through 582 removed outlier: 4.103A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 588 removed outlier: 4.127A pdb=" N LEU B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 588' Processing helix chain 'B' and resid 590 through 605 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.983A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 612 " --> pdb=" O HIS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.953A pdb=" N LEU B 637 " --> pdb=" O CYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 809 removed outlier: 3.702A pdb=" N GLY B 809 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 878 through 901 removed outlier: 3.911A pdb=" N LYS B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.897A pdb=" N ASN B 930 " --> pdb=" O GLU B 926 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1012 Processing helix chain 'B' and resid 1029 through 1033 removed outlier: 4.104A pdb=" N VAL B1033 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1060 removed outlier: 3.758A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA B1053 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B1054 " --> pdb=" O LEU B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1643 through 1647 removed outlier: 3.561A pdb=" N THR B1646 " --> pdb=" O LEU B1643 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1647 " --> pdb=" O GLU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1643 through 1647' Processing helix chain 'B' and resid 1648 through 1665 Processing helix chain 'B' and resid 1671 through 1681 removed outlier: 3.857A pdb=" N SER B1679 " --> pdb=" O HIS B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1683 through 1692 removed outlier: 4.365A pdb=" N LEU B1687 " --> pdb=" O GLU B1683 " (cutoff:3.500A) Processing helix chain 'B' and resid 1697 through 1711 removed outlier: 3.547A pdb=" N HIS B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1712 through 1722 removed outlier: 3.532A pdb=" N MET B1722 " --> pdb=" O ALA B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1737 removed outlier: 3.743A pdb=" N ILE B1737 " --> pdb=" O THR B1734 " (cutoff:3.500A) Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.658A pdb=" N LEU B1788 " --> pdb=" O PRO B1784 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B1805 " --> pdb=" O LYS B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1833 Proline residue: B1821 - end of helix removed outlier: 3.664A pdb=" N GLY B1833 " --> pdb=" O LEU B1829 " (cutoff:3.500A) Processing helix chain 'B' and resid 1836 through 1848 removed outlier: 3.613A pdb=" N ILE B1847 " --> pdb=" O ILE B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1898 through 1949 removed outlier: 3.571A pdb=" N GLN B1916 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B1930 " --> pdb=" O ALA B1926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B1937 " --> pdb=" O ALA B1933 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B1938 " --> pdb=" O LYS B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1955 through 1965 removed outlier: 4.659A pdb=" N ARG B1962 " --> pdb=" O ALA B1958 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B1963 " --> pdb=" O ARG B1959 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B1964 " --> pdb=" O LYS B1960 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1976 Processing helix chain 'B' and resid 1989 through 2006 removed outlier: 3.967A pdb=" N ASP B1993 " --> pdb=" O GLU B1989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2072 removed outlier: 3.691A pdb=" N VAL B2066 " --> pdb=" O SER B2062 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B2069 " --> pdb=" O MET B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2093 removed outlier: 3.853A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2101 removed outlier: 3.907A pdb=" N LEU B2097 " --> pdb=" O GLY B2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2130 Processing helix chain 'B' and resid 2134 through 2151 Processing helix chain 'B' and resid 2152 through 2157 removed outlier: 3.817A pdb=" N GLN B2156 " --> pdb=" O LYS B2152 " (cutoff:3.500A) Processing helix chain 'B' and resid 2157 through 2165 removed outlier: 3.633A pdb=" N MET B2161 " --> pdb=" O HIS B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2179 removed outlier: 4.237A pdb=" N ASN B2176 " --> pdb=" O GLU B2172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B2177 " --> pdb=" O VAL B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2188 through 2205 Processing helix chain 'B' and resid 2208 through 2223 removed outlier: 3.744A pdb=" N ASP B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS B2216 " --> pdb=" O ALA B2212 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B2218 " --> pdb=" O PHE B2214 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR B2219 " --> pdb=" O ASP B2215 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B2222 " --> pdb=" O SER B2218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B2223 " --> pdb=" O TYR B2219 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2247 Processing helix chain 'B' and resid 2249 through 2256 Processing helix chain 'B' and resid 2260 through 2274 Processing helix chain 'B' and resid 2276 through 2283 Processing helix chain 'B' and resid 2292 through 2305 Processing helix chain 'B' and resid 2312 through 2326 Processing helix chain 'B' and resid 2327 through 2330 Processing helix chain 'B' and resid 2341 through 2355 Processing helix chain 'B' and resid 2356 through 2359 removed outlier: 3.825A pdb=" N ASP B2359 " --> pdb=" O PRO B2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2356 through 2359' Processing helix chain 'B' and resid 2382 through 2401 Processing helix chain 'B' and resid 2413 through 2426 Processing helix chain 'B' and resid 2427 through 2436 Processing helix chain 'B' and resid 2462 through 2475 removed outlier: 3.938A pdb=" N ALA B2466 " --> pdb=" O ASP B2462 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2479 through 2491 Processing helix chain 'B' and resid 2491 through 2500 Processing helix chain 'B' and resid 2507 through 2524 removed outlier: 3.798A pdb=" N UNK B2511 " --> pdb=" O SER B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2533 through 2547 Processing helix chain 'B' and resid 2553 through 2571 Processing helix chain 'B' and resid 2575 through 2589 Processing helix chain 'B' and resid 2594 through 2612 Processing helix chain 'B' and resid 2617 through 2635 removed outlier: 3.513A pdb=" N UNK B2621 " --> pdb=" O UNK B2617 " (cutoff:3.500A) Processing helix chain 'B' and resid 2641 through 2649 removed outlier: 3.922A pdb=" N UNK B2645 " --> pdb=" O UNK B2641 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK B2646 " --> pdb=" O UNK B2642 " (cutoff:3.500A) Processing helix chain 'B' and resid 2650 through 2657 Processing helix chain 'B' and resid 2713 through 2739 removed outlier: 4.085A pdb=" N ASN B2721 " --> pdb=" O GLU B2717 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B2722 " --> pdb=" O TYR B2718 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2769 removed outlier: 3.939A pdb=" N GLU B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2772 through 2784 removed outlier: 4.234A pdb=" N GLU B2776 " --> pdb=" O TRP B2772 " (cutoff:3.500A) Processing helix chain 'B' and resid 2836 through 2863 Processing helix chain 'B' and resid 2877 through 2898 removed outlier: 3.787A pdb=" N ASP B2884 " --> pdb=" O GLU B2880 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B2887 " --> pdb=" O LYS B2883 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE B2894 " --> pdb=" O ASP B2890 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B2895 " --> pdb=" O ILE B2891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2917 through 2941 Processing helix chain 'B' and resid 2962 through 2982 removed outlier: 4.349A pdb=" N UNK B2975 " --> pdb=" O UNK B2971 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N UNK B2976 " --> pdb=" O UNK B2972 " (cutoff:3.500A) Processing helix chain 'B' and resid 2992 through 3007 Processing helix chain 'B' and resid 3015 through 3029 Processing helix chain 'B' and resid 3105 through 3129 removed outlier: 3.776A pdb=" N UNK B3120 " --> pdb=" O UNK B3116 " (cutoff:3.500A) Processing helix chain 'B' and resid 3137 through 3157 removed outlier: 4.213A pdb=" N UNK B3156 " --> pdb=" O UNK B3152 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK B3157 " --> pdb=" O UNK B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3163 through 3182 Processing helix chain 'B' and resid 3183 through 3200 removed outlier: 3.627A pdb=" N UNK B3187 " --> pdb=" O UNK B3183 " (cutoff:3.500A) Processing helix chain 'B' and resid 3208 through 3220 removed outlier: 3.689A pdb=" N UNK B3219 " --> pdb=" O UNK B3215 " (cutoff:3.500A) Processing helix chain 'B' and resid 3232 through 3251 Processing helix chain 'B' and resid 3255 through 3270 Processing helix chain 'B' and resid 3271 through 3277 Processing helix chain 'B' and resid 3281 through 3296 removed outlier: 4.122A pdb=" N UNK B3285 " --> pdb=" O UNK B3281 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3315 Processing helix chain 'B' and resid 3324 through 3356 Processing helix chain 'B' and resid 3362 through 3388 removed outlier: 4.132A pdb=" N UNK B3383 " --> pdb=" O UNK B3379 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3391 No H-bonds generated for 'chain 'B' and resid 3389 through 3391' Processing helix chain 'B' and resid 3400 through 3420 removed outlier: 4.158A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3434 removed outlier: 4.517A pdb=" N UNK B3428 " --> pdb=" O UNK B3424 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK B3429 " --> pdb=" O UNK B3425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3478 through 3496 removed outlier: 4.274A pdb=" N UNK B3495 " --> pdb=" O UNK B3491 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK B3496 " --> pdb=" O UNK B3492 " (cutoff:3.500A) Processing helix chain 'B' and resid 3503 through 3514 Processing helix chain 'B' and resid 3516 through 3527 removed outlier: 3.854A pdb=" N UNK B3527 " --> pdb=" O UNK B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3541 through 3548 removed outlier: 4.138A pdb=" N UNK B3545 " --> pdb=" O UNK B3541 " (cutoff:3.500A) Processing helix chain 'B' and resid 3555 through 3579 Processing helix chain 'B' and resid 3612 through 3627 removed outlier: 3.823A pdb=" N VAL B3616 " --> pdb=" O ARG B3612 " (cutoff:3.500A) Processing helix chain 'B' and resid 3637 through 3644 Processing helix chain 'B' and resid 3661 through 3676 Processing helix chain 'B' and resid 3684 through 3698 removed outlier: 3.513A pdb=" N ASP B3692 " --> pdb=" O MET B3688 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS B3698 " --> pdb=" O MET B3694 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3732 removed outlier: 3.768A pdb=" N GLU B3719 " --> pdb=" O GLU B3715 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B3730 " --> pdb=" O GLN B3726 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B3732 " --> pdb=" O ALA B3728 " (cutoff:3.500A) Processing helix chain 'B' and resid 3734 through 3745 removed outlier: 3.553A pdb=" N LEU B3740 " --> pdb=" O ALA B3736 " (cutoff:3.500A) Processing helix chain 'B' and resid 3751 through 3766 removed outlier: 3.576A pdb=" N LYS B3759 " --> pdb=" O ALA B3755 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3783 Processing helix chain 'B' and resid 3788 through 3797 Processing helix chain 'B' and resid 3803 through 3817 Processing helix chain 'B' and resid 3824 through 3828 Processing helix chain 'B' and resid 3831 through 3847 removed outlier: 3.699A pdb=" N CYS B3846 " --> pdb=" O LEU B3842 " (cutoff:3.500A) Processing helix chain 'B' and resid 3850 through 3859 Processing helix chain 'B' and resid 3868 through 3891 removed outlier: 3.718A pdb=" N TYR B3891 " --> pdb=" O PHE B3887 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3923 removed outlier: 4.183A pdb=" N PHE B3905 " --> pdb=" O GLY B3901 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B3908 " --> pdb=" O ASN B3904 " (cutoff:3.500A) Processing helix chain 'B' and resid 3927 through 3936 Processing helix chain 'B' and resid 3938 through 3959 removed outlier: 3.599A pdb=" N HIS B3952 " --> pdb=" O HIS B3948 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B3955 " --> pdb=" O ALA B3951 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) Processing helix chain 'B' and resid 3963 through 3984 Processing helix chain 'B' and resid 3992 through 4005 removed outlier: 3.513A pdb=" N LYS B3996 " --> pdb=" O GLY B3992 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4021 Processing helix chain 'B' and resid 4022 through 4027 removed outlier: 3.803A pdb=" N SER B4027 " --> pdb=" O LYS B4023 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4035 removed outlier: 4.520A pdb=" N ASP B4035 " --> pdb=" O PHE B4031 " (cutoff:3.500A) Processing helix chain 'B' and resid 4044 through 4054 removed outlier: 3.728A pdb=" N HIS B4048 " --> pdb=" O LYS B4044 " (cutoff:3.500A) Processing helix chain 'B' and resid 4058 through 4069 Processing helix chain 'B' and resid 4078 through 4087 Processing helix chain 'B' and resid 4087 through 4108 Processing helix chain 'B' and resid 4111 through 4126 removed outlier: 3.727A pdb=" N PHE B4117 " --> pdb=" O ARG B4113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B4120 " --> pdb=" O THR B4116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER B4123 " --> pdb=" O GLU B4119 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL B4124 " --> pdb=" O LEU B4120 " (cutoff:3.500A) Processing helix chain 'B' and resid 4128 through 4130 No H-bonds generated for 'chain 'B' and resid 4128 through 4130' Processing helix chain 'B' and resid 4152 through 4160 removed outlier: 3.612A pdb=" N GLU B4160 " --> pdb=" O ARG B4156 " (cutoff:3.500A) Processing helix chain 'B' and resid 4161 through 4178 removed outlier: 3.758A pdb=" N GLU B4178 " --> pdb=" O ASP B4174 " (cutoff:3.500A) Processing helix chain 'B' and resid 4183 through 4204 Processing helix chain 'B' and resid 4276 through 4285 removed outlier: 3.996A pdb=" N LEU B4280 " --> pdb=" O LYS B4276 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B4285 " --> pdb=" O ALA B4281 " (cutoff:3.500A) Processing helix chain 'B' and resid 4286 through 4302 removed outlier: 3.714A pdb=" N THR B4292 " --> pdb=" O SER B4288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B4300 " --> pdb=" O PHE B4296 " (cutoff:3.500A) Processing helix chain 'B' and resid 4304 through 4309 Processing helix chain 'B' and resid 4479 through 4496 removed outlier: 3.812A pdb=" N TYR B4485 " --> pdb=" O LYS B4481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B4488 " --> pdb=" O ALA B4484 " (cutoff:3.500A) Processing helix chain 'B' and resid 4496 through 4515 Processing helix chain 'B' and resid 4567 through 4593 removed outlier: 3.862A pdb=" N ARG B4572 " --> pdb=" O GLU B4568 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B4590 " --> pdb=" O ILE B4586 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS B4591 " --> pdb=" O ILE B4587 " (cutoff:3.500A) Processing helix chain 'B' and resid 4593 through 4613 Processing helix chain 'B' and resid 4613 through 4618 Processing helix chain 'B' and resid 4624 through 4630 removed outlier: 3.957A pdb=" N GLN B4628 " --> pdb=" O ASP B4624 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4661 through 4670 removed outlier: 4.223A pdb=" N SER B4666 " --> pdb=" O ARG B4662 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B4668 " --> pdb=" O ARG B4664 " (cutoff:3.500A) Processing helix chain 'B' and resid 4671 through 4682 Processing helix chain 'B' and resid 4702 through 4715 Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 3.756A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4742 Processing helix chain 'B' and resid 4743 through 4748 Processing helix chain 'B' and resid 4749 through 4751 No H-bonds generated for 'chain 'B' and resid 4749 through 4751' Processing helix chain 'B' and resid 4752 through 4761 removed outlier: 4.257A pdb=" N SER B4758 " --> pdb=" O THR B4754 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B4759 " --> pdb=" O ILE B4755 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4807 through 4819 Processing helix chain 'B' and resid 4838 through 4854 removed outlier: 3.522A pdb=" N ILE B4854 " --> pdb=" O PHE B4850 " (cutoff:3.500A) Processing helix chain 'B' and resid 4857 through 4886 removed outlier: 3.740A pdb=" N ILE B4861 " --> pdb=" O LEU B4857 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B4869 " --> pdb=" O ILE B4865 " (cutoff:3.500A) Processing helix chain 'B' and resid 4893 through 4898 removed outlier: 3.942A pdb=" N PHE B4897 " --> pdb=" O GLY B4893 " (cutoff:3.500A) Processing helix chain 'B' and resid 4902 through 4910 Processing helix chain 'B' and resid 4913 through 4928 removed outlier: 4.478A pdb=" N ASP B4928 " --> pdb=" O LEU B4924 " (cutoff:3.500A) Processing helix chain 'B' and resid 4933 through 4946 Processing helix chain 'B' and resid 4956 through 4961 Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 75 through 84 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.501A pdb=" N VAL C 269 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.998A pdb=" N LYS C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 322 " --> pdb=" O LYS C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 322' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.624A pdb=" N ARG C 383 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.715A pdb=" N LEU C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.568A pdb=" N GLU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.625A pdb=" N ASP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 541 removed outlier: 4.744A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.903A pdb=" N CYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 561 Processing helix chain 'C' and resid 562 through 565 removed outlier: 4.377A pdb=" N LEU C 565 " --> pdb=" O LEU C 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 565' Processing helix chain 'C' and resid 567 through 582 removed outlier: 4.102A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 582 " --> pdb=" O VAL C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 588 removed outlier: 4.129A pdb=" N LEU C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 582 through 588' Processing helix chain 'C' and resid 590 through 605 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.983A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 612 " --> pdb=" O HIS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.953A pdb=" N LEU C 637 " --> pdb=" O CYS C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 809 removed outlier: 3.702A pdb=" N GLY C 809 " --> pdb=" O GLY C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 Processing helix chain 'C' and resid 875 through 877 No H-bonds generated for 'chain 'C' and resid 875 through 877' Processing helix chain 'C' and resid 878 through 901 removed outlier: 3.911A pdb=" N LYS C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.896A pdb=" N ASN C 930 " --> pdb=" O GLU C 926 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN C 932 " --> pdb=" O GLU C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1012 Processing helix chain 'C' and resid 1029 through 1033 removed outlier: 4.105A pdb=" N VAL C1033 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1060 removed outlier: 3.758A pdb=" N ASN C1046 " --> pdb=" O THR C1042 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA C1053 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 Processing helix chain 'C' and resid 1643 through 1647 removed outlier: 3.561A pdb=" N THR C1646 " --> pdb=" O LEU C1643 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C1647 " --> pdb=" O GLU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1643 through 1647' Processing helix chain 'C' and resid 1648 through 1665 Processing helix chain 'C' and resid 1671 through 1681 removed outlier: 3.857A pdb=" N SER C1679 " --> pdb=" O HIS C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1683 through 1692 removed outlier: 4.365A pdb=" N LEU C1687 " --> pdb=" O GLU C1683 " (cutoff:3.500A) Processing helix chain 'C' and resid 1697 through 1711 removed outlier: 3.546A pdb=" N HIS C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) Processing helix chain 'C' and resid 1712 through 1722 removed outlier: 3.533A pdb=" N MET C1722 " --> pdb=" O ALA C1718 " (cutoff:3.500A) Processing helix chain 'C' and resid 1733 through 1737 removed outlier: 3.743A pdb=" N ILE C1737 " --> pdb=" O THR C1734 " (cutoff:3.500A) Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.658A pdb=" N LEU C1788 " --> pdb=" O PRO C1784 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C1805 " --> pdb=" O LYS C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1833 Proline residue: C1821 - end of helix removed outlier: 3.664A pdb=" N GLY C1833 " --> pdb=" O LEU C1829 " (cutoff:3.500A) Processing helix chain 'C' and resid 1836 through 1848 removed outlier: 3.612A pdb=" N ILE C1847 " --> pdb=" O ILE C1843 " (cutoff:3.500A) Processing helix chain 'C' and resid 1898 through 1949 removed outlier: 3.570A pdb=" N GLN C1916 " --> pdb=" O LEU C1912 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C1930 " --> pdb=" O ALA C1926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C1937 " --> pdb=" O ALA C1933 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN C1938 " --> pdb=" O LYS C1934 " (cutoff:3.500A) Processing helix chain 'C' and resid 1955 through 1965 removed outlier: 4.660A pdb=" N ARG C1962 " --> pdb=" O ALA C1958 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU C1963 " --> pdb=" O ARG C1959 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C1964 " --> pdb=" O LYS C1960 " (cutoff:3.500A) Processing helix chain 'C' and resid 1967 through 1976 Processing helix chain 'C' and resid 1989 through 2006 removed outlier: 3.967A pdb=" N ASP C1993 " --> pdb=" O GLU C1989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2072 removed outlier: 3.689A pdb=" N VAL C2066 " --> pdb=" O SER C2062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C2069 " --> pdb=" O MET C2065 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2093 removed outlier: 3.852A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2101 removed outlier: 3.907A pdb=" N LEU C2097 " --> pdb=" O GLY C2093 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2130 Processing helix chain 'C' and resid 2134 through 2151 Processing helix chain 'C' and resid 2152 through 2157 removed outlier: 3.817A pdb=" N GLN C2156 " --> pdb=" O LYS C2152 " (cutoff:3.500A) Processing helix chain 'C' and resid 2157 through 2165 removed outlier: 3.633A pdb=" N MET C2161 " --> pdb=" O HIS C2157 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2179 removed outlier: 4.236A pdb=" N ASN C2176 " --> pdb=" O GLU C2172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C2177 " --> pdb=" O VAL C2173 " (cutoff:3.500A) Processing helix chain 'C' and resid 2188 through 2205 Processing helix chain 'C' and resid 2208 through 2223 removed outlier: 3.743A pdb=" N ASP C2215 " --> pdb=" O LYS C2211 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS C2216 " --> pdb=" O ALA C2212 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER C2218 " --> pdb=" O PHE C2214 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR C2219 " --> pdb=" O ASP C2215 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C2222 " --> pdb=" O SER C2218 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C2223 " --> pdb=" O TYR C2219 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2247 Processing helix chain 'C' and resid 2249 through 2256 Processing helix chain 'C' and resid 2260 through 2274 Processing helix chain 'C' and resid 2276 through 2283 Processing helix chain 'C' and resid 2292 through 2305 Processing helix chain 'C' and resid 2312 through 2326 Processing helix chain 'C' and resid 2327 through 2330 Processing helix chain 'C' and resid 2341 through 2355 Processing helix chain 'C' and resid 2356 through 2359 removed outlier: 3.825A pdb=" N ASP C2359 " --> pdb=" O PRO C2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2356 through 2359' Processing helix chain 'C' and resid 2382 through 2401 Processing helix chain 'C' and resid 2413 through 2426 Processing helix chain 'C' and resid 2427 through 2436 Processing helix chain 'C' and resid 2462 through 2475 removed outlier: 3.937A pdb=" N ALA C2466 " --> pdb=" O ASP C2462 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET C2467 " --> pdb=" O HIS C2463 " (cutoff:3.500A) Processing helix chain 'C' and resid 2479 through 2491 Processing helix chain 'C' and resid 2491 through 2500 Processing helix chain 'C' and resid 2507 through 2524 removed outlier: 3.797A pdb=" N UNK C2511 " --> pdb=" O SER C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2533 through 2547 Processing helix chain 'C' and resid 2553 through 2571 Processing helix chain 'C' and resid 2575 through 2589 Processing helix chain 'C' and resid 2594 through 2612 Processing helix chain 'C' and resid 2617 through 2635 removed outlier: 3.513A pdb=" N UNK C2621 " --> pdb=" O UNK C2617 " (cutoff:3.500A) Processing helix chain 'C' and resid 2641 through 2649 removed outlier: 3.922A pdb=" N UNK C2645 " --> pdb=" O UNK C2641 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNK C2646 " --> pdb=" O UNK C2642 " (cutoff:3.500A) Processing helix chain 'C' and resid 2650 through 2657 Processing helix chain 'C' and resid 2713 through 2739 removed outlier: 4.084A pdb=" N ASN C2721 " --> pdb=" O GLU C2717 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C2722 " --> pdb=" O TYR C2718 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2769 removed outlier: 3.939A pdb=" N GLU C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) Processing helix chain 'C' and resid 2772 through 2784 removed outlier: 4.234A pdb=" N GLU C2776 " --> pdb=" O TRP C2772 " (cutoff:3.500A) Processing helix chain 'C' and resid 2836 through 2863 Processing helix chain 'C' and resid 2877 through 2898 removed outlier: 3.788A pdb=" N ASP C2884 " --> pdb=" O GLU C2880 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C2887 " --> pdb=" O LYS C2883 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE C2894 " --> pdb=" O ASP C2890 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C2895 " --> pdb=" O ILE C2891 " (cutoff:3.500A) Processing helix chain 'C' and resid 2917 through 2941 Processing helix chain 'C' and resid 2962 through 2982 removed outlier: 4.348A pdb=" N UNK C2975 " --> pdb=" O UNK C2971 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N UNK C2976 " --> pdb=" O UNK C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3007 Processing helix chain 'C' and resid 3015 through 3029 Processing helix chain 'C' and resid 3105 through 3129 removed outlier: 3.775A pdb=" N UNK C3120 " --> pdb=" O UNK C3116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3137 through 3157 removed outlier: 4.213A pdb=" N UNK C3156 " --> pdb=" O UNK C3152 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK C3157 " --> pdb=" O UNK C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3163 through 3182 Processing helix chain 'C' and resid 3183 through 3200 removed outlier: 3.628A pdb=" N UNK C3187 " --> pdb=" O UNK C3183 " (cutoff:3.500A) Processing helix chain 'C' and resid 3208 through 3220 removed outlier: 3.689A pdb=" N UNK C3219 " --> pdb=" O UNK C3215 " (cutoff:3.500A) Processing helix chain 'C' and resid 3232 through 3251 Processing helix chain 'C' and resid 3255 through 3270 Processing helix chain 'C' and resid 3271 through 3277 Processing helix chain 'C' and resid 3281 through 3296 removed outlier: 4.122A pdb=" N UNK C3285 " --> pdb=" O UNK C3281 " (cutoff:3.500A) Processing helix chain 'C' and resid 3301 through 3315 Processing helix chain 'C' and resid 3324 through 3356 Processing helix chain 'C' and resid 3362 through 3388 removed outlier: 4.133A pdb=" N UNK C3383 " --> pdb=" O UNK C3379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3389 through 3391 No H-bonds generated for 'chain 'C' and resid 3389 through 3391' Processing helix chain 'C' and resid 3400 through 3420 removed outlier: 4.158A pdb=" N UNK C3404 " --> pdb=" O UNK C3400 " (cutoff:3.500A) Processing helix chain 'C' and resid 3421 through 3434 removed outlier: 4.516A pdb=" N UNK C3428 " --> pdb=" O UNK C3424 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK C3429 " --> pdb=" O UNK C3425 " (cutoff:3.500A) Processing helix chain 'C' and resid 3478 through 3496 removed outlier: 4.274A pdb=" N UNK C3495 " --> pdb=" O UNK C3491 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N UNK C3496 " --> pdb=" O UNK C3492 " (cutoff:3.500A) Processing helix chain 'C' and resid 3503 through 3514 Processing helix chain 'C' and resid 3516 through 3527 removed outlier: 3.854A pdb=" N UNK C3527 " --> pdb=" O UNK C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3541 through 3548 removed outlier: 4.137A pdb=" N UNK C3545 " --> pdb=" O UNK C3541 " (cutoff:3.500A) Processing helix chain 'C' and resid 3555 through 3579 Processing helix chain 'C' and resid 3612 through 3627 removed outlier: 3.823A pdb=" N VAL C3616 " --> pdb=" O ARG C3612 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3644 Processing helix chain 'C' and resid 3661 through 3676 Processing helix chain 'C' and resid 3684 through 3698 removed outlier: 3.513A pdb=" N ASP C3692 " --> pdb=" O MET C3688 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS C3698 " --> pdb=" O MET C3694 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3732 removed outlier: 3.768A pdb=" N GLU C3719 " --> pdb=" O GLU C3715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C3730 " --> pdb=" O GLN C3726 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP C3732 " --> pdb=" O ALA C3728 " (cutoff:3.500A) Processing helix chain 'C' and resid 3734 through 3745 removed outlier: 3.553A pdb=" N LEU C3740 " --> pdb=" O ALA C3736 " (cutoff:3.500A) Processing helix chain 'C' and resid 3751 through 3766 removed outlier: 3.575A pdb=" N LYS C3759 " --> pdb=" O ALA C3755 " (cutoff:3.500A) Processing helix chain 'C' and resid 3769 through 3783 Processing helix chain 'C' and resid 3788 through 3797 Processing helix chain 'C' and resid 3803 through 3817 Processing helix chain 'C' and resid 3824 through 3828 Processing helix chain 'C' and resid 3831 through 3847 removed outlier: 3.699A pdb=" N CYS C3846 " --> pdb=" O LEU C3842 " (cutoff:3.500A) Processing helix chain 'C' and resid 3850 through 3859 Processing helix chain 'C' and resid 3868 through 3891 removed outlier: 3.717A pdb=" N TYR C3891 " --> pdb=" O PHE C3887 " (cutoff:3.500A) Processing helix chain 'C' and resid 3898 through 3923 removed outlier: 4.183A pdb=" N PHE C3905 " --> pdb=" O GLY C3901 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C3908 " --> pdb=" O ASN C3904 " (cutoff:3.500A) Processing helix chain 'C' and resid 3927 through 3936 Processing helix chain 'C' and resid 3938 through 3959 removed outlier: 3.599A pdb=" N HIS C3952 " --> pdb=" O HIS C3948 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET C3955 " --> pdb=" O ALA C3951 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C3959 " --> pdb=" O MET C3955 " (cutoff:3.500A) Processing helix chain 'C' and resid 3963 through 3984 Processing helix chain 'C' and resid 3992 through 4005 removed outlier: 3.513A pdb=" N LYS C3996 " --> pdb=" O GLY C3992 " (cutoff:3.500A) Processing helix chain 'C' and resid 4005 through 4021 Processing helix chain 'C' and resid 4022 through 4027 removed outlier: 3.803A pdb=" N SER C4027 " --> pdb=" O LYS C4023 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4035 removed outlier: 4.520A pdb=" N ASP C4035 " --> pdb=" O PHE C4031 " (cutoff:3.500A) Processing helix chain 'C' and resid 4044 through 4054 removed outlier: 3.727A pdb=" N HIS C4048 " --> pdb=" O LYS C4044 " (cutoff:3.500A) Processing helix chain 'C' and resid 4058 through 4069 Processing helix chain 'C' and resid 4078 through 4087 Processing helix chain 'C' and resid 4087 through 4108 Processing helix chain 'C' and resid 4111 through 4126 removed outlier: 3.727A pdb=" N PHE C4117 " --> pdb=" O ARG C4113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C4120 " --> pdb=" O THR C4116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER C4123 " --> pdb=" O GLU C4119 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL C4124 " --> pdb=" O LEU C4120 " (cutoff:3.500A) Processing helix chain 'C' and resid 4128 through 4130 No H-bonds generated for 'chain 'C' and resid 4128 through 4130' Processing helix chain 'C' and resid 4152 through 4160 removed outlier: 3.611A pdb=" N GLU C4160 " --> pdb=" O ARG C4156 " (cutoff:3.500A) Processing helix chain 'C' and resid 4161 through 4178 removed outlier: 3.758A pdb=" N GLU C4178 " --> pdb=" O ASP C4174 " (cutoff:3.500A) Processing helix chain 'C' and resid 4183 through 4204 Processing helix chain 'C' and resid 4276 through 4285 removed outlier: 3.996A pdb=" N LEU C4280 " --> pdb=" O LYS C4276 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C4285 " --> pdb=" O ALA C4281 " (cutoff:3.500A) Processing helix chain 'C' and resid 4286 through 4302 removed outlier: 3.714A pdb=" N THR C4292 " --> pdb=" O SER C4288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C4300 " --> pdb=" O PHE C4296 " (cutoff:3.500A) Processing helix chain 'C' and resid 4304 through 4309 Processing helix chain 'C' and resid 4479 through 4496 removed outlier: 3.812A pdb=" N TYR C4485 " --> pdb=" O LYS C4481 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C4488 " --> pdb=" O ALA C4484 " (cutoff:3.500A) Processing helix chain 'C' and resid 4496 through 4515 Processing helix chain 'C' and resid 4567 through 4593 removed outlier: 3.863A pdb=" N ARG C4572 " --> pdb=" O GLU C4568 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C4590 " --> pdb=" O ILE C4586 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C4591 " --> pdb=" O ILE C4587 " (cutoff:3.500A) Processing helix chain 'C' and resid 4593 through 4613 Processing helix chain 'C' and resid 4613 through 4618 Processing helix chain 'C' and resid 4624 through 4630 removed outlier: 3.958A pdb=" N GLN C4628 " --> pdb=" O ASP C4624 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4661 through 4670 removed outlier: 4.223A pdb=" N SER C4666 " --> pdb=" O ARG C4662 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C4668 " --> pdb=" O ARG C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4671 through 4682 Processing helix chain 'C' and resid 4702 through 4715 Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 3.756A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4742 Processing helix chain 'C' and resid 4743 through 4748 Processing helix chain 'C' and resid 4749 through 4751 No H-bonds generated for 'chain 'C' and resid 4749 through 4751' Processing helix chain 'C' and resid 4752 through 4761 removed outlier: 4.257A pdb=" N SER C4758 " --> pdb=" O THR C4754 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL C4759 " --> pdb=" O ILE C4755 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4807 through 4819 Processing helix chain 'C' and resid 4838 through 4854 removed outlier: 3.523A pdb=" N ILE C4854 " --> pdb=" O PHE C4850 " (cutoff:3.500A) Processing helix chain 'C' and resid 4857 through 4886 removed outlier: 3.740A pdb=" N ILE C4861 " --> pdb=" O LEU C4857 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C4869 " --> pdb=" O ILE C4865 " (cutoff:3.500A) Processing helix chain 'C' and resid 4893 through 4898 removed outlier: 3.943A pdb=" N PHE C4897 " --> pdb=" O GLY C4893 " (cutoff:3.500A) Processing helix chain 'C' and resid 4902 through 4910 Processing helix chain 'C' and resid 4913 through 4928 removed outlier: 4.478A pdb=" N ASP C4928 " --> pdb=" O LEU C4924 " (cutoff:3.500A) Processing helix chain 'C' and resid 4933 through 4946 Processing helix chain 'C' and resid 4956 through 4961 Processing helix chain 'I' and resid 57 through 66 Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.501A pdb=" N VAL D 269 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS D 270 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 270' Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.998A pdb=" N LYS D 321 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 322 " --> pdb=" O LYS D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 322' Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 379 through 383 removed outlier: 3.623A pdb=" N ARG D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.715A pdb=" N LEU D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 463 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.568A pdb=" N GLU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 506 Processing helix chain 'D' and resid 510 through 519 removed outlier: 3.625A pdb=" N ASP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 541 removed outlier: 4.743A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.903A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 561 Processing helix chain 'D' and resid 562 through 565 removed outlier: 4.376A pdb=" N LEU D 565 " --> pdb=" O LEU D 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 562 through 565' Processing helix chain 'D' and resid 567 through 582 removed outlier: 4.102A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 582 " --> pdb=" O VAL D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 588 removed outlier: 4.128A pdb=" N LEU D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 582 through 588' Processing helix chain 'D' and resid 590 through 605 Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.982A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.953A pdb=" N LEU D 637 " --> pdb=" O CYS D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 809 removed outlier: 3.701A pdb=" N GLY D 809 " --> pdb=" O GLY D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 878 through 901 removed outlier: 3.911A pdb=" N LYS D 897 " --> pdb=" O TRP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 3.897A pdb=" N ASN D 930 " --> pdb=" O GLU D 926 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN D 932 " --> pdb=" O GLU D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1012 Processing helix chain 'D' and resid 1029 through 1033 removed outlier: 4.104A pdb=" N VAL D1033 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1060 removed outlier: 3.758A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA D1053 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D1054 " --> pdb=" O LEU D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1643 through 1647 removed outlier: 3.560A pdb=" N THR D1646 " --> pdb=" O LEU D1643 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D1647 " --> pdb=" O GLU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1643 through 1647' Processing helix chain 'D' and resid 1648 through 1665 Processing helix chain 'D' and resid 1671 through 1681 removed outlier: 3.856A pdb=" N SER D1679 " --> pdb=" O HIS D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1683 through 1692 removed outlier: 4.365A pdb=" N LEU D1687 " --> pdb=" O GLU D1683 " (cutoff:3.500A) Processing helix chain 'D' and resid 1697 through 1711 removed outlier: 3.547A pdb=" N HIS D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) Processing helix chain 'D' and resid 1712 through 1722 removed outlier: 3.533A pdb=" N MET D1722 " --> pdb=" O ALA D1718 " (cutoff:3.500A) Processing helix chain 'D' and resid 1733 through 1737 removed outlier: 3.744A pdb=" N ILE D1737 " --> pdb=" O THR D1734 " (cutoff:3.500A) Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.658A pdb=" N LEU D1788 " --> pdb=" O PRO D1784 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D1805 " --> pdb=" O LYS D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1833 Proline residue: D1821 - end of helix removed outlier: 3.664A pdb=" N GLY D1833 " --> pdb=" O LEU D1829 " (cutoff:3.500A) Processing helix chain 'D' and resid 1836 through 1848 removed outlier: 3.612A pdb=" N ILE D1847 " --> pdb=" O ILE D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1898 through 1949 removed outlier: 3.571A pdb=" N GLN D1916 " --> pdb=" O LEU D1912 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP D1930 " --> pdb=" O ALA D1926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D1937 " --> pdb=" O ALA D1933 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN D1938 " --> pdb=" O LYS D1934 " (cutoff:3.500A) Processing helix chain 'D' and resid 1955 through 1965 removed outlier: 4.660A pdb=" N ARG D1962 " --> pdb=" O ALA D1958 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU D1963 " --> pdb=" O ARG D1959 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D1964 " --> pdb=" O LYS D1960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1967 through 1976 Processing helix chain 'D' and resid 1989 through 2006 removed outlier: 3.968A pdb=" N ASP D1993 " --> pdb=" O GLU D1989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2072 removed outlier: 3.690A pdb=" N VAL D2066 " --> pdb=" O SER D2062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D2069 " --> pdb=" O MET D2065 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2093 removed outlier: 3.852A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2101 removed outlier: 3.906A pdb=" N LEU D2097 " --> pdb=" O GLY D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2130 Processing helix chain 'D' and resid 2134 through 2151 Processing helix chain 'D' and resid 2152 through 2157 removed outlier: 3.817A pdb=" N GLN D2156 " --> pdb=" O LYS D2152 " (cutoff:3.500A) Processing helix chain 'D' and resid 2157 through 2165 removed outlier: 3.632A pdb=" N MET D2161 " --> pdb=" O HIS D2157 " (cutoff:3.500A) Processing helix chain 'D' and resid 2165 through 2179 removed outlier: 4.237A pdb=" N ASN D2176 " --> pdb=" O GLU D2172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D2177 " --> pdb=" O VAL D2173 " (cutoff:3.500A) Processing helix chain 'D' and resid 2188 through 2205 Processing helix chain 'D' and resid 2208 through 2223 removed outlier: 3.743A pdb=" N ASP D2215 " --> pdb=" O LYS D2211 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS D2216 " --> pdb=" O ALA D2212 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER D2218 " --> pdb=" O PHE D2214 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR D2219 " --> pdb=" O ASP D2215 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D2222 " --> pdb=" O SER D2218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D2223 " --> pdb=" O TYR D2219 " (cutoff:3.500A) Processing helix chain 'D' and resid 2237 through 2247 Processing helix chain 'D' and resid 2249 through 2256 Processing helix chain 'D' and resid 2260 through 2274 Processing helix chain 'D' and resid 2276 through 2283 Processing helix chain 'D' and resid 2292 through 2305 Processing helix chain 'D' and resid 2312 through 2326 Processing helix chain 'D' and resid 2327 through 2330 Processing helix chain 'D' and resid 2341 through 2355 Processing helix chain 'D' and resid 2356 through 2359 removed outlier: 3.824A pdb=" N ASP D2359 " --> pdb=" O PRO D2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2356 through 2359' Processing helix chain 'D' and resid 2382 through 2401 Processing helix chain 'D' and resid 2413 through 2426 Processing helix chain 'D' and resid 2427 through 2436 Processing helix chain 'D' and resid 2462 through 2475 removed outlier: 3.938A pdb=" N ALA D2466 " --> pdb=" O ASP D2462 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET D2467 " --> pdb=" O HIS D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2479 through 2491 Processing helix chain 'D' and resid 2491 through 2500 Processing helix chain 'D' and resid 2507 through 2524 removed outlier: 3.798A pdb=" N UNK D2511 " --> pdb=" O SER D2507 " (cutoff:3.500A) Processing helix chain 'D' and resid 2533 through 2547 Processing helix chain 'D' and resid 2553 through 2571 Processing helix chain 'D' and resid 2575 through 2589 Processing helix chain 'D' and resid 2594 through 2612 Processing helix chain 'D' and resid 2617 through 2635 removed outlier: 3.512A pdb=" N UNK D2621 " --> pdb=" O UNK D2617 " (cutoff:3.500A) Processing helix chain 'D' and resid 2641 through 2649 removed outlier: 3.923A pdb=" N UNK D2645 " --> pdb=" O UNK D2641 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNK D2646 " --> pdb=" O UNK D2642 " (cutoff:3.500A) Processing helix chain 'D' and resid 2650 through 2657 Processing helix chain 'D' and resid 2713 through 2739 removed outlier: 4.084A pdb=" N ASN D2721 " --> pdb=" O GLU D2717 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS D2722 " --> pdb=" O TYR D2718 " (cutoff:3.500A) Processing helix chain 'D' and resid 2763 through 2769 removed outlier: 3.938A pdb=" N GLU D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) Processing helix chain 'D' and resid 2772 through 2784 removed outlier: 4.234A pdb=" N GLU D2776 " --> pdb=" O TRP D2772 " (cutoff:3.500A) Processing helix chain 'D' and resid 2836 through 2863 Processing helix chain 'D' and resid 2877 through 2898 removed outlier: 3.787A pdb=" N ASP D2884 " --> pdb=" O GLU D2880 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D2887 " --> pdb=" O LYS D2883 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE D2894 " --> pdb=" O ASP D2890 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D2895 " --> pdb=" O ILE D2891 " (cutoff:3.500A) Processing helix chain 'D' and resid 2917 through 2941 Processing helix chain 'D' and resid 2962 through 2982 removed outlier: 4.348A pdb=" N UNK D2975 " --> pdb=" O UNK D2971 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N UNK D2976 " --> pdb=" O UNK D2972 " (cutoff:3.500A) Processing helix chain 'D' and resid 2992 through 3007 Processing helix chain 'D' and resid 3015 through 3029 Processing helix chain 'D' and resid 3105 through 3129 removed outlier: 3.776A pdb=" N UNK D3120 " --> pdb=" O UNK D3116 " (cutoff:3.500A) Processing helix chain 'D' and resid 3137 through 3157 removed outlier: 4.213A pdb=" N UNK D3156 " --> pdb=" O UNK D3152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N UNK D3157 " --> pdb=" O UNK D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3163 through 3182 Processing helix chain 'D' and resid 3183 through 3200 removed outlier: 3.628A pdb=" N UNK D3187 " --> pdb=" O UNK D3183 " (cutoff:3.500A) Processing helix chain 'D' and resid 3208 through 3220 removed outlier: 3.689A pdb=" N UNK D3219 " --> pdb=" O UNK D3215 " (cutoff:3.500A) Processing helix chain 'D' and resid 3232 through 3251 Processing helix chain 'D' and resid 3255 through 3270 Processing helix chain 'D' and resid 3271 through 3277 Processing helix chain 'D' and resid 3281 through 3296 removed outlier: 4.122A pdb=" N UNK D3285 " --> pdb=" O UNK D3281 " (cutoff:3.500A) Processing helix chain 'D' and resid 3301 through 3315 Processing helix chain 'D' and resid 3324 through 3356 Processing helix chain 'D' and resid 3362 through 3388 removed outlier: 4.132A pdb=" N UNK D3383 " --> pdb=" O UNK D3379 " (cutoff:3.500A) Processing helix chain 'D' and resid 3389 through 3391 No H-bonds generated for 'chain 'D' and resid 3389 through 3391' Processing helix chain 'D' and resid 3400 through 3420 removed outlier: 4.158A pdb=" N UNK D3404 " --> pdb=" O UNK D3400 " (cutoff:3.500A) Processing helix chain 'D' and resid 3421 through 3434 removed outlier: 4.517A pdb=" N UNK D3428 " --> pdb=" O UNK D3424 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N UNK D3429 " --> pdb=" O UNK D3425 " (cutoff:3.500A) Processing helix chain 'D' and resid 3478 through 3496 removed outlier: 4.275A pdb=" N UNK D3495 " --> pdb=" O UNK D3491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK D3496 " --> pdb=" O UNK D3492 " (cutoff:3.500A) Processing helix chain 'D' and resid 3503 through 3514 Processing helix chain 'D' and resid 3516 through 3527 removed outlier: 3.853A pdb=" N UNK D3527 " --> pdb=" O UNK D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3541 through 3548 removed outlier: 4.137A pdb=" N UNK D3545 " --> pdb=" O UNK D3541 " (cutoff:3.500A) Processing helix chain 'D' and resid 3555 through 3579 Processing helix chain 'D' and resid 3612 through 3627 removed outlier: 3.824A pdb=" N VAL D3616 " --> pdb=" O ARG D3612 " (cutoff:3.500A) Processing helix chain 'D' and resid 3637 through 3644 Processing helix chain 'D' and resid 3661 through 3676 Processing helix chain 'D' and resid 3684 through 3698 removed outlier: 3.513A pdb=" N ASP D3692 " --> pdb=" O MET D3688 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS D3698 " --> pdb=" O MET D3694 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3732 removed outlier: 3.768A pdb=" N GLU D3719 " --> pdb=" O GLU D3715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU D3730 " --> pdb=" O GLN D3726 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D3732 " --> pdb=" O ALA D3728 " (cutoff:3.500A) Processing helix chain 'D' and resid 3734 through 3745 removed outlier: 3.552A pdb=" N LEU D3740 " --> pdb=" O ALA D3736 " (cutoff:3.500A) Processing helix chain 'D' and resid 3751 through 3766 removed outlier: 3.575A pdb=" N LYS D3759 " --> pdb=" O ALA D3755 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3783 Processing helix chain 'D' and resid 3788 through 3797 Processing helix chain 'D' and resid 3803 through 3817 Processing helix chain 'D' and resid 3824 through 3828 Processing helix chain 'D' and resid 3831 through 3847 removed outlier: 3.700A pdb=" N CYS D3846 " --> pdb=" O LEU D3842 " (cutoff:3.500A) Processing helix chain 'D' and resid 3850 through 3859 Processing helix chain 'D' and resid 3868 through 3891 removed outlier: 3.718A pdb=" N TYR D3891 " --> pdb=" O PHE D3887 " (cutoff:3.500A) Processing helix chain 'D' and resid 3898 through 3923 removed outlier: 4.182A pdb=" N PHE D3905 " --> pdb=" O GLY D3901 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D3908 " --> pdb=" O ASN D3904 " (cutoff:3.500A) Processing helix chain 'D' and resid 3927 through 3936 Processing helix chain 'D' and resid 3938 through 3959 removed outlier: 3.599A pdb=" N HIS D3952 " --> pdb=" O HIS D3948 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET D3955 " --> pdb=" O ALA D3951 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D3959 " --> pdb=" O MET D3955 " (cutoff:3.500A) Processing helix chain 'D' and resid 3963 through 3984 Processing helix chain 'D' and resid 3992 through 4005 removed outlier: 3.513A pdb=" N LYS D3996 " --> pdb=" O GLY D3992 " (cutoff:3.500A) Processing helix chain 'D' and resid 4005 through 4021 Processing helix chain 'D' and resid 4022 through 4027 removed outlier: 3.803A pdb=" N SER D4027 " --> pdb=" O LYS D4023 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4035 removed outlier: 4.520A pdb=" N ASP D4035 " --> pdb=" O PHE D4031 " (cutoff:3.500A) Processing helix chain 'D' and resid 4044 through 4054 removed outlier: 3.727A pdb=" N HIS D4048 " --> pdb=" O LYS D4044 " (cutoff:3.500A) Processing helix chain 'D' and resid 4058 through 4069 Processing helix chain 'D' and resid 4078 through 4087 Processing helix chain 'D' and resid 4087 through 4108 Processing helix chain 'D' and resid 4111 through 4126 removed outlier: 3.728A pdb=" N PHE D4117 " --> pdb=" O ARG D4113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D4120 " --> pdb=" O THR D4116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER D4123 " --> pdb=" O GLU D4119 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL D4124 " --> pdb=" O LEU D4120 " (cutoff:3.500A) Processing helix chain 'D' and resid 4128 through 4130 No H-bonds generated for 'chain 'D' and resid 4128 through 4130' Processing helix chain 'D' and resid 4152 through 4160 removed outlier: 3.612A pdb=" N GLU D4160 " --> pdb=" O ARG D4156 " (cutoff:3.500A) Processing helix chain 'D' and resid 4161 through 4178 removed outlier: 3.758A pdb=" N GLU D4178 " --> pdb=" O ASP D4174 " (cutoff:3.500A) Processing helix chain 'D' and resid 4183 through 4204 Processing helix chain 'D' and resid 4276 through 4285 removed outlier: 3.995A pdb=" N LEU D4280 " --> pdb=" O LYS D4276 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D4285 " --> pdb=" O ALA D4281 " (cutoff:3.500A) Processing helix chain 'D' and resid 4286 through 4302 removed outlier: 3.714A pdb=" N THR D4292 " --> pdb=" O SER D4288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D4300 " --> pdb=" O PHE D4296 " (cutoff:3.500A) Processing helix chain 'D' and resid 4304 through 4309 Processing helix chain 'D' and resid 4479 through 4496 removed outlier: 3.812A pdb=" N TYR D4485 " --> pdb=" O LYS D4481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D4488 " --> pdb=" O ALA D4484 " (cutoff:3.500A) Processing helix chain 'D' and resid 4496 through 4515 Processing helix chain 'D' and resid 4567 through 4593 removed outlier: 3.863A pdb=" N ARG D4572 " --> pdb=" O GLU D4568 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR D4590 " --> pdb=" O ILE D4586 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D4591 " --> pdb=" O ILE D4587 " (cutoff:3.500A) Processing helix chain 'D' and resid 4593 through 4613 Processing helix chain 'D' and resid 4613 through 4618 Processing helix chain 'D' and resid 4624 through 4630 removed outlier: 3.958A pdb=" N GLN D4628 " --> pdb=" O ASP D4624 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4661 through 4670 removed outlier: 4.224A pdb=" N SER D4666 " --> pdb=" O ARG D4662 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D4668 " --> pdb=" O ARG D4664 " (cutoff:3.500A) Processing helix chain 'D' and resid 4671 through 4682 Processing helix chain 'D' and resid 4702 through 4715 Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 3.755A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4742 Processing helix chain 'D' and resid 4743 through 4748 Processing helix chain 'D' and resid 4749 through 4751 No H-bonds generated for 'chain 'D' and resid 4749 through 4751' Processing helix chain 'D' and resid 4752 through 4761 removed outlier: 4.257A pdb=" N SER D4758 " --> pdb=" O THR D4754 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D4759 " --> pdb=" O ILE D4755 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4807 through 4819 Processing helix chain 'D' and resid 4838 through 4854 removed outlier: 3.521A pdb=" N ILE D4854 " --> pdb=" O PHE D4850 " (cutoff:3.500A) Processing helix chain 'D' and resid 4857 through 4886 removed outlier: 3.740A pdb=" N ILE D4861 " --> pdb=" O LEU D4857 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D4869 " --> pdb=" O ILE D4865 " (cutoff:3.500A) Processing helix chain 'D' and resid 4893 through 4898 removed outlier: 3.942A pdb=" N PHE D4897 " --> pdb=" O GLY D4893 " (cutoff:3.500A) Processing helix chain 'D' and resid 4902 through 4910 Processing helix chain 'D' and resid 4913 through 4928 removed outlier: 4.477A pdb=" N ASP D4928 " --> pdb=" O LEU D4924 " (cutoff:3.500A) Processing helix chain 'D' and resid 4933 through 4946 Processing helix chain 'D' and resid 4956 through 4961 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.374A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.260A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 203 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 299 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.539A pdb=" N ARG A 389 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA7, first strand: chain 'A' and resid 645 through 650 removed outlier: 3.609A pdb=" N GLN A 645 " --> pdb=" O HIS A1632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 738 through 740 Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 774 removed outlier: 3.607A pdb=" N GLN A 773 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AB4, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 5.464A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1258 through 1260 Processing sheet with id=AB6, first strand: chain 'A' and resid 1269 through 1273 removed outlier: 3.536A pdb=" N ILE A1273 " --> pdb=" O GLN A1287 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A1287 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1299 through 1303 Processing sheet with id=AB8, first strand: chain 'A' and resid 1299 through 1303 removed outlier: 3.835A pdb=" N ALA A1377 " --> pdb=" O UNK A1420 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N UNK A1420 " --> pdb=" O ALA A1377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1317 through 1320 Processing sheet with id=AC1, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.039A pdb=" N LYS A1363 " --> pdb=" O ASP A1357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1726 through 1728 Processing sheet with id=AC3, first strand: chain 'A' and resid 2306 through 2307 Processing sheet with id=AC4, first strand: chain 'A' and resid 2741 through 2742 removed outlier: 5.807A pdb=" N ILE A2741 " --> pdb=" O GLN A2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 4132 through 4138 removed outlier: 3.745A pdb=" N PHE A4149 " --> pdb=" O GLY A4133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 4519 through 4520 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 9 removed outlier: 6.451A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 9 removed outlier: 6.451A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU G 107 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR G 22 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.375A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG B 122 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 69 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 129 through 132 removed outlier: 4.258A pdb=" N VAL B 147 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 203 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 295 through 299 Processing sheet with id=AD3, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.538A pdb=" N ARG B 389 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 305 through 307 Processing sheet with id=AD5, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AD6, first strand: chain 'B' and resid 645 through 650 removed outlier: 3.609A pdb=" N GLN B 645 " --> pdb=" O HIS B1632 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 738 through 740 Processing sheet with id=AD8, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.607A pdb=" N GLN B 773 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 850 through 851 Processing sheet with id=AE2, first strand: chain 'B' and resid 850 through 851 Processing sheet with id=AE3, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 5.464A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1258 through 1260 Processing sheet with id=AE5, first strand: chain 'B' and resid 1269 through 1273 removed outlier: 3.536A pdb=" N ILE B1273 " --> pdb=" O GLN B1287 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN B1287 " --> pdb=" O ILE B1273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1299 through 1303 Processing sheet with id=AE7, first strand: chain 'B' and resid 1299 through 1303 removed outlier: 3.836A pdb=" N ALA B1377 " --> pdb=" O UNK B1420 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N UNK B1420 " --> pdb=" O ALA B1377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1317 through 1320 Processing sheet with id=AE9, first strand: chain 'B' and resid 1353 through 1358 removed outlier: 4.038A pdb=" N LYS B1363 " --> pdb=" O ASP B1357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1726 through 1728 Processing sheet with id=AF2, first strand: chain 'B' and resid 2306 through 2307 Processing sheet with id=AF3, first strand: chain 'B' and resid 2741 through 2742 removed outlier: 5.806A pdb=" N ILE B2741 " --> pdb=" O GLN B2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 4132 through 4138 removed outlier: 3.745A pdb=" N PHE B4149 " --> pdb=" O GLY B4133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 4519 through 4520 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.451A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.451A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU H 107 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR H 22 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 51 removed outlier: 5.374A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG C 122 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 69 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 129 through 132 removed outlier: 4.259A pdb=" N VAL C 147 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 203 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 295 through 299 Processing sheet with id=AG2, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.539A pdb=" N ARG C 389 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 305 through 307 Processing sheet with id=AG4, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AG5, first strand: chain 'C' and resid 645 through 650 removed outlier: 3.609A pdb=" N GLN C 645 " --> pdb=" O HIS C1632 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 738 through 740 Processing sheet with id=AG7, first strand: chain 'C' and resid 773 through 774 removed outlier: 3.607A pdb=" N GLN C 773 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AG9, first strand: chain 'C' and resid 850 through 851 Processing sheet with id=AH1, first strand: chain 'C' and resid 850 through 851 Processing sheet with id=AH2, first strand: chain 'C' and resid 1149 through 1151 removed outlier: 5.464A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AH4, first strand: chain 'C' and resid 1269 through 1273 removed outlier: 3.536A pdb=" N ILE C1273 " --> pdb=" O GLN C1287 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN C1287 " --> pdb=" O ILE C1273 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1299 through 1303 Processing sheet with id=AH6, first strand: chain 'C' and resid 1299 through 1303 removed outlier: 3.835A pdb=" N ALA C1377 " --> pdb=" O UNK C1420 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N UNK C1420 " --> pdb=" O ALA C1377 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 1317 through 1320 Processing sheet with id=AH8, first strand: chain 'C' and resid 1353 through 1358 removed outlier: 4.039A pdb=" N LYS C1363 " --> pdb=" O ASP C1357 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1726 through 1728 Processing sheet with id=AI1, first strand: chain 'C' and resid 2306 through 2307 Processing sheet with id=AI2, first strand: chain 'C' and resid 2741 through 2742 removed outlier: 5.807A pdb=" N ILE C2741 " --> pdb=" O GLN C2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'C' and resid 4132 through 4138 removed outlier: 3.745A pdb=" N PHE C4149 " --> pdb=" O GLY C4133 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 4519 through 4520 Processing sheet with id=AI5, first strand: chain 'I' and resid 4 through 9 removed outlier: 6.450A pdb=" N ARG I 72 " --> pdb=" O ILE I 8 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 4 through 9 removed outlier: 6.450A pdb=" N ARG I 72 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL I 24 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU I 107 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR I 22 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 48 through 51 removed outlier: 5.374A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 129 through 132 removed outlier: 4.258A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 295 through 299 Processing sheet with id=AJ1, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.539A pdb=" N ARG D 389 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 305 through 307 Processing sheet with id=AJ3, first strand: chain 'D' and resid 329 through 332 Processing sheet with id=AJ4, first strand: chain 'D' and resid 645 through 650 removed outlier: 3.609A pdb=" N GLN D 645 " --> pdb=" O HIS D1632 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 738 through 740 Processing sheet with id=AJ6, first strand: chain 'D' and resid 773 through 774 removed outlier: 3.607A pdb=" N GLN D 773 " --> pdb=" O ILE D 770 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AJ8, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=AJ9, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=AK1, first strand: chain 'D' and resid 1149 through 1151 removed outlier: 5.464A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 1258 through 1260 Processing sheet with id=AK3, first strand: chain 'D' and resid 1269 through 1273 removed outlier: 3.537A pdb=" N ILE D1273 " --> pdb=" O GLN D1287 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN D1287 " --> pdb=" O ILE D1273 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 1299 through 1303 Processing sheet with id=AK5, first strand: chain 'D' and resid 1299 through 1303 removed outlier: 3.834A pdb=" N ALA D1377 " --> pdb=" O UNK D1420 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N UNK D1420 " --> pdb=" O ALA D1377 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 1317 through 1320 Processing sheet with id=AK7, first strand: chain 'D' and resid 1353 through 1358 removed outlier: 4.038A pdb=" N LYS D1363 " --> pdb=" O ASP D1357 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 1726 through 1728 Processing sheet with id=AK9, first strand: chain 'D' and resid 2306 through 2307 Processing sheet with id=AL1, first strand: chain 'D' and resid 2741 through 2742 removed outlier: 5.808A pdb=" N ILE D2741 " --> pdb=" O GLN D2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL1 Processing sheet with id=AL2, first strand: chain 'D' and resid 4132 through 4138 removed outlier: 3.745A pdb=" N PHE D4149 " --> pdb=" O GLY D4133 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 4519 through 4520 Processing sheet with id=AL4, first strand: chain 'J' and resid 4 through 9 removed outlier: 6.450A pdb=" N ARG J 72 " --> pdb=" O ILE J 8 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 4 through 9 removed outlier: 6.450A pdb=" N ARG J 72 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL J 24 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU J 107 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR J 22 " --> pdb=" O LEU J 107 " (cutoff:3.500A) 7268 hydrogen bonds defined for protein. 21132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 91.87 Time building geometry restraints manager: 37.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 41597 1.34 - 1.47: 28818 1.47 - 1.59: 54269 1.59 - 1.71: 8 1.71 - 1.84: 1168 Bond restraints: 125860 Sorted by residual: bond pdb=" CA MET C2233 " pdb=" CB MET C2233 " ideal model delta sigma weight residual 1.526 1.608 -0.082 1.70e-02 3.46e+03 2.32e+01 bond pdb=" CA MET D2233 " pdb=" CB MET D2233 " ideal model delta sigma weight residual 1.526 1.608 -0.082 1.70e-02 3.46e+03 2.30e+01 bond pdb=" CA MET B2233 " pdb=" CB MET B2233 " ideal model delta sigma weight residual 1.526 1.608 -0.081 1.70e-02 3.46e+03 2.29e+01 bond pdb=" CA MET A2233 " pdb=" CB MET A2233 " ideal model delta sigma weight residual 1.526 1.607 -0.081 1.70e-02 3.46e+03 2.28e+01 bond pdb=" CB MET C2233 " pdb=" CG MET C2233 " ideal model delta sigma weight residual 1.520 1.611 -0.091 3.00e-02 1.11e+03 9.14e+00 ... (remaining 125855 not shown) Histogram of bond angle deviations from ideal: 96.87 - 105.66: 2044 105.66 - 114.44: 74127 114.44 - 123.22: 89851 123.22 - 132.00: 4450 132.00 - 140.78: 176 Bond angle restraints: 170648 Sorted by residual: angle pdb=" CB MET A2233 " pdb=" CG MET A2233 " pdb=" SD MET A2233 " ideal model delta sigma weight residual 112.70 140.78 -28.08 3.00e+00 1.11e-01 8.76e+01 angle pdb=" CB MET D2233 " pdb=" CG MET D2233 " pdb=" SD MET D2233 " ideal model delta sigma weight residual 112.70 140.78 -28.08 3.00e+00 1.11e-01 8.76e+01 angle pdb=" CB MET C2233 " pdb=" CG MET C2233 " pdb=" SD MET C2233 " ideal model delta sigma weight residual 112.70 140.76 -28.06 3.00e+00 1.11e-01 8.75e+01 angle pdb=" CB MET B2233 " pdb=" CG MET B2233 " pdb=" SD MET B2233 " ideal model delta sigma weight residual 112.70 140.74 -28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" CA MET B2233 " pdb=" CB MET B2233 " pdb=" CG MET B2233 " ideal model delta sigma weight residual 114.10 128.83 -14.73 2.00e+00 2.50e-01 5.43e+01 ... (remaining 170643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 68463 17.93 - 35.86: 5511 35.86 - 53.80: 1059 53.80 - 71.73: 291 71.73 - 89.66: 140 Dihedral angle restraints: 75464 sinusoidal: 27060 harmonic: 48404 Sorted by residual: dihedral pdb=" CA GLU B2172 " pdb=" C GLU B2172 " pdb=" N VAL B2173 " pdb=" CA VAL B2173 " ideal model delta harmonic sigma weight residual 180.00 147.09 32.91 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA GLU D2172 " pdb=" C GLU D2172 " pdb=" N VAL D2173 " pdb=" CA VAL D2173 " ideal model delta harmonic sigma weight residual 180.00 147.13 32.87 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLU C2172 " pdb=" C GLU C2172 " pdb=" N VAL C2173 " pdb=" CA VAL C2173 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 75461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 16020 0.049 - 0.098: 2776 0.098 - 0.147: 556 0.147 - 0.197: 40 0.197 - 0.246: 12 Chirality restraints: 19404 Sorted by residual: chirality pdb=" CG LEU C1190 " pdb=" CB LEU C1190 " pdb=" CD1 LEU C1190 " pdb=" CD2 LEU C1190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR A 646 " pdb=" CA THR A 646 " pdb=" OG1 THR A 646 " pdb=" CG2 THR A 646 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A1190 " pdb=" CB LEU A1190 " pdb=" CD1 LEU A1190 " pdb=" CD2 LEU A1190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 19401 not shown) Planarity restraints: 22256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D2258 " 0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO D2259 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D2259 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D2259 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A2258 " -0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A2259 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A2259 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A2259 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C2258 " 0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO C2259 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C2259 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C2259 " 0.054 5.00e-02 4.00e+02 ... (remaining 22253 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1654 2.66 - 3.22: 118003 3.22 - 3.78: 194613 3.78 - 4.34: 251181 4.34 - 4.90: 410917 Nonbonded interactions: 976368 Sorted by model distance: nonbonded pdb=" OG1 THR D 973 " pdb=" O TYR D 976 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR B 973 " pdb=" O TYR B 976 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR C 973 " pdb=" O TYR C 976 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR A 973 " pdb=" O TYR A 976 " model vdw 2.100 2.440 nonbonded pdb=" O PHE C1769 " pdb=" OH TYR I 83 " model vdw 2.115 2.440 ... (remaining 976363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 11.860 Check model and map are aligned: 1.280 Set scattering table: 0.830 Process input model: 290.660 Find NCS groups from input model: 5.360 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 314.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 125860 Z= 0.181 Angle : 0.661 28.082 170648 Z= 0.344 Chirality : 0.039 0.246 19404 Planarity : 0.005 0.111 22256 Dihedral : 14.556 89.658 44016 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.87 % Allowed : 1.48 % Favored : 96.64 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.07), residues: 13424 helix: 1.10 (0.07), residues: 6556 sheet: -1.51 (0.13), residues: 1512 loop : -2.11 (0.08), residues: 5356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C3889 HIS 0.013 0.001 HIS A 747 PHE 0.056 0.001 PHE C 768 TYR 0.033 0.001 TYR B4780 ARG 0.018 0.001 ARG A2335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1167 time to evaluate : 9.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.5795 (pt0) cc_final: 0.5336 (pt0) REVERT: A 331 PHE cc_start: 0.4386 (m-80) cc_final: 0.4131 (m-80) REVERT: A 655 MET cc_start: 0.7290 (mmm) cc_final: 0.6820 (mmt) REVERT: A 846 TYR cc_start: 0.5129 (p90) cc_final: 0.4632 (p90) REVERT: A 1123 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7014 (tt0) REVERT: A 1174 MET cc_start: 0.7202 (mtp) cc_final: 0.6836 (mtm) REVERT: A 1209 VAL cc_start: 0.8134 (t) cc_final: 0.7743 (t) REVERT: A 1983 SER cc_start: 0.6519 (t) cc_final: 0.6283 (t) REVERT: A 2065 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7734 (mmm) REVERT: A 2352 ILE cc_start: 0.6980 (mm) cc_final: 0.6525 (mm) REVERT: A 2425 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6529 (mt) REVERT: A 2781 MET cc_start: 0.0997 (ttp) cc_final: 0.0617 (ptp) REVERT: A 3896 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6371 (tp) REVERT: A 4881 GLU cc_start: 0.7580 (tp30) cc_final: 0.7331 (tp30) REVERT: G 44 ASN cc_start: 0.7923 (m110) cc_final: 0.7690 (t0) REVERT: B 1174 MET cc_start: 0.6875 (mtp) cc_final: 0.6564 (mtm) REVERT: B 2065 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7267 (mmm) REVERT: B 2335 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.5512 (tpt90) REVERT: B 2781 MET cc_start: 0.2245 (ttp) cc_final: -0.0271 (mtt) REVERT: B 2842 MET cc_start: 0.1346 (OUTLIER) cc_final: -0.0121 (mmm) REVERT: B 4885 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8008 (p) REVERT: H 44 ASN cc_start: 0.7956 (m110) cc_final: 0.7724 (t0) REVERT: C 79 GLN cc_start: 0.6205 (pt0) cc_final: 0.5804 (pt0) REVERT: C 655 MET cc_start: 0.7505 (mmm) cc_final: 0.6867 (mmt) REVERT: C 995 MET cc_start: 0.2205 (mmp) cc_final: 0.1161 (mtp) REVERT: C 1123 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6906 (mt0) REVERT: C 1165 MET cc_start: 0.6629 (mtm) cc_final: 0.6338 (mtp) REVERT: C 1174 MET cc_start: 0.6770 (mtp) cc_final: 0.6367 (mtm) REVERT: C 1215 MET cc_start: 0.6462 (tpp) cc_final: 0.6106 (tpp) REVERT: C 1300 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5016 (mtp) REVERT: C 1722 MET cc_start: 0.7811 (mmt) cc_final: 0.7580 (mmt) REVERT: C 1734 THR cc_start: 0.6148 (m) cc_final: 0.5766 (m) REVERT: C 2149 MET cc_start: 0.7968 (mmt) cc_final: 0.7549 (mmt) REVERT: C 2265 VAL cc_start: 0.7535 (t) cc_final: 0.7264 (t) REVERT: C 2352 ILE cc_start: 0.7340 (mm) cc_final: 0.6973 (mm) REVERT: C 2387 ILE cc_start: 0.8522 (mt) cc_final: 0.8321 (mt) REVERT: C 2425 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6583 (mt) REVERT: C 2756 MET cc_start: 0.1686 (mmt) cc_final: 0.0960 (mmt) REVERT: C 2781 MET cc_start: -0.0670 (ttp) cc_final: -0.2142 (mtt) REVERT: C 2842 MET cc_start: 0.1253 (OUTLIER) cc_final: -0.0775 (mmm) REVERT: C 4854 ILE cc_start: 0.8386 (pt) cc_final: 0.8165 (pt) REVERT: D 79 GLN cc_start: 0.5485 (pt0) cc_final: 0.5063 (pt0) REVERT: D 655 MET cc_start: 0.7232 (mmm) cc_final: 0.6756 (mmt) REVERT: D 846 TYR cc_start: 0.4735 (p90) cc_final: 0.4252 (p90) REVERT: D 1174 MET cc_start: 0.7235 (mtp) cc_final: 0.6790 (mtm) REVERT: D 1209 VAL cc_start: 0.8096 (t) cc_final: 0.7721 (t) REVERT: D 1956 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.3816 (mp) REVERT: D 2491 PHE cc_start: 0.5747 (m-80) cc_final: 0.5342 (m-10) REVERT: D 2781 MET cc_start: 0.1634 (ttp) cc_final: 0.1238 (ptp) REVERT: D 4808 MET cc_start: 0.8626 (tpt) cc_final: 0.8422 (tpp) REVERT: J 44 ASN cc_start: 0.7846 (m110) cc_final: 0.7556 (t0) outliers start: 221 outliers final: 49 residues processed: 1269 average time/residue: 0.9454 time to fit residues: 2146.3267 Evaluate side-chains 900 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 840 time to evaluate : 9.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1226 TYR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1743 GLU Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2233 MET Chi-restraints excluded: chain A residue 2277 GLN Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2478 GLU Chi-restraints excluded: chain A residue 3885 SER Chi-restraints excluded: chain A residue 3896 ILE Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain B residue 1152 TYR Chi-restraints excluded: chain B residue 1226 TYR Chi-restraints excluded: chain B residue 1743 GLU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2065 MET Chi-restraints excluded: chain B residue 2191 MET Chi-restraints excluded: chain B residue 2233 MET Chi-restraints excluded: chain B residue 2335 ARG Chi-restraints excluded: chain B residue 2478 GLU Chi-restraints excluded: chain B residue 2842 MET Chi-restraints excluded: chain B residue 3885 SER Chi-restraints excluded: chain B residue 4001 MET Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4885 THR Chi-restraints excluded: chain C residue 1152 TYR Chi-restraints excluded: chain C residue 1226 TYR Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 2004 THR Chi-restraints excluded: chain C residue 2233 MET Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2478 GLU Chi-restraints excluded: chain C residue 2842 MET Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 1152 TYR Chi-restraints excluded: chain D residue 1161 VAL Chi-restraints excluded: chain D residue 1226 TYR Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1743 GLU Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1956 LEU Chi-restraints excluded: chain D residue 2004 THR Chi-restraints excluded: chain D residue 2191 MET Chi-restraints excluded: chain D residue 2233 MET Chi-restraints excluded: chain D residue 2320 VAL Chi-restraints excluded: chain D residue 2478 GLU Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3889 TRP Chi-restraints excluded: chain D residue 4045 ARG Chi-restraints excluded: chain D residue 4782 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1398 optimal weight: 3.9990 chunk 1255 optimal weight: 20.0000 chunk 696 optimal weight: 30.0000 chunk 428 optimal weight: 9.9990 chunk 846 optimal weight: 0.5980 chunk 670 optimal weight: 50.0000 chunk 1297 optimal weight: 10.0000 chunk 502 optimal weight: 30.0000 chunk 789 optimal weight: 9.9990 chunk 966 optimal weight: 5.9990 chunk 1503 optimal weight: 30.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS A 645 GLN A1171 HIS ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2385 ASN A2480 GLN ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3948 HIS A3963 GLN A3974 GLN A4129 GLN B 117 HIS B 645 GLN B 681 HIS ** B1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS B1627 GLN ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2480 GLN ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3948 HIS B3963 GLN B4129 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C1171 HIS ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2274 GLN ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3948 HIS ** C3954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4129 GLN C4786 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 202 HIS D 645 GLN D1171 HIS D1627 GLN ** D1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1969 GLN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2385 ASN ** D2480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3954 GLN D3974 GLN D4129 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 125860 Z= 0.420 Angle : 0.689 9.972 170648 Z= 0.354 Chirality : 0.043 0.333 19404 Planarity : 0.005 0.081 22256 Dihedral : 5.207 62.770 17781 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.13 % Favored : 92.86 % Rotamer: Outliers : 1.36 % Allowed : 8.93 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.07), residues: 13424 helix: 0.73 (0.06), residues: 6608 sheet: -1.42 (0.13), residues: 1400 loop : -2.22 (0.08), residues: 5416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 557 HIS 0.019 0.002 HIS A1680 PHE 0.031 0.003 PHE D1740 TYR 0.037 0.002 TYR C4780 ARG 0.016 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 892 time to evaluate : 9.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.5818 (pt0) cc_final: 0.5542 (pt0) REVERT: A 331 PHE cc_start: 0.4411 (m-80) cc_final: 0.4104 (m-80) REVERT: A 655 MET cc_start: 0.7166 (mmm) cc_final: 0.6577 (mmt) REVERT: A 1123 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6916 (mt0) REVERT: A 1174 MET cc_start: 0.7394 (mtp) cc_final: 0.7034 (mtm) REVERT: A 2133 MET cc_start: 0.8327 (tpt) cc_final: 0.7990 (mmm) REVERT: A 2385 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6618 (t0) REVERT: A 2781 MET cc_start: 0.0793 (ttp) cc_final: 0.0423 (ptm) REVERT: A 2843 MET cc_start: 0.0050 (tpp) cc_final: -0.0434 (ttp) REVERT: A 4480 LYS cc_start: 0.5703 (mptt) cc_final: 0.4311 (mmmt) REVERT: A 4706 MET cc_start: 0.7111 (mmp) cc_final: 0.6865 (mmm) REVERT: G 44 ASN cc_start: 0.8028 (m110) cc_final: 0.7814 (t0) REVERT: B 79 GLN cc_start: 0.5354 (pt0) cc_final: 0.5039 (pt0) REVERT: B 1174 MET cc_start: 0.6870 (mtp) cc_final: 0.6484 (mtm) REVERT: B 2003 MET cc_start: 0.8032 (mmm) cc_final: 0.7337 (mmt) REVERT: B 2278 MET cc_start: 0.7383 (mmt) cc_final: 0.7114 (tpt) REVERT: B 2756 MET cc_start: 0.0842 (mmt) cc_final: 0.0526 (mmt) REVERT: B 2781 MET cc_start: 0.2105 (ttp) cc_final: -0.0008 (mtt) REVERT: H 44 ASN cc_start: 0.8057 (m110) cc_final: 0.7849 (t0) REVERT: C 79 GLN cc_start: 0.6150 (pt0) cc_final: 0.5691 (pt0) REVERT: C 655 MET cc_start: 0.7337 (mmm) cc_final: 0.6658 (mmt) REVERT: C 1165 MET cc_start: 0.6623 (mtm) cc_final: 0.6298 (mtp) REVERT: C 1174 MET cc_start: 0.6822 (mtp) cc_final: 0.6387 (mtm) REVERT: C 1215 MET cc_start: 0.6717 (tpp) cc_final: 0.6460 (tpp) REVERT: C 1772 ILE cc_start: 0.6799 (tp) cc_final: 0.6465 (mt) REVERT: C 1844 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7861 (mt) REVERT: C 2003 MET cc_start: 0.8281 (mmm) cc_final: 0.7791 (mmp) REVERT: C 2352 ILE cc_start: 0.6726 (mm) cc_final: 0.6416 (mm) REVERT: C 2387 ILE cc_start: 0.8711 (mt) cc_final: 0.8435 (mt) REVERT: C 2756 MET cc_start: 0.2342 (mmt) cc_final: 0.1833 (mmt) REVERT: C 2781 MET cc_start: -0.0953 (ttp) cc_final: -0.2378 (mtt) REVERT: C 2843 MET cc_start: 0.1349 (tpt) cc_final: 0.0961 (tpt) REVERT: I 6 GLU cc_start: 0.7114 (tt0) cc_final: 0.6882 (mp0) REVERT: I 44 ASN cc_start: 0.8052 (m110) cc_final: 0.7729 (t0) REVERT: D 79 GLN cc_start: 0.5546 (pt0) cc_final: 0.5159 (pt0) REVERT: D 241 MET cc_start: 0.1887 (OUTLIER) cc_final: 0.1549 (mtp) REVERT: D 655 MET cc_start: 0.7311 (mmm) cc_final: 0.6511 (mmt) REVERT: D 1174 MET cc_start: 0.7357 (mtp) cc_final: 0.7005 (mtm) REVERT: D 1960 LYS cc_start: 0.4574 (mmtm) cc_final: 0.3545 (mmtp) REVERT: D 2133 MET cc_start: 0.8241 (tpt) cc_final: 0.8013 (mmm) REVERT: D 2385 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6626 (t0) REVERT: D 2491 PHE cc_start: 0.5809 (m-80) cc_final: 0.5202 (m-10) REVERT: D 2756 MET cc_start: 0.0754 (mmt) cc_final: 0.0510 (mmt) REVERT: D 2781 MET cc_start: 0.1695 (ttp) cc_final: 0.1266 (ptp) REVERT: D 2843 MET cc_start: 0.0224 (OUTLIER) cc_final: -0.0682 (ttp) outliers start: 160 outliers final: 96 residues processed: 999 average time/residue: 0.9482 time to fit residues: 1702.6750 Evaluate side-chains 901 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 800 time to evaluate : 8.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2385 ASN Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3885 SER Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3885 SER Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4288 SER Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4663 ASP Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1844 LEU Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2407 LEU Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2478 GLU Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 1161 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 2240 ASP Chi-restraints excluded: chain D residue 2385 ASN Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4288 SER Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 835 optimal weight: 20.0000 chunk 466 optimal weight: 0.8980 chunk 1251 optimal weight: 9.9990 chunk 1024 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 1506 optimal weight: 40.0000 chunk 1627 optimal weight: 2.9990 chunk 1341 optimal weight: 40.0000 chunk 1493 optimal weight: 30.0000 chunk 513 optimal weight: 8.9990 chunk 1208 optimal weight: 5.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN A 651 HIS ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 GLN ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 GLN ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 ASN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4096 ASN ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 240 HIS B 651 HIS B1951 ASN ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2277 GLN B2385 ASN ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3633 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3954 GLN B3974 GLN B4096 ASN ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS C 476 GLN ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1711 HIS ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3633 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3954 GLN C3974 GLN C4096 ASN ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS D 651 HIS D1123 GLN ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1951 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2846 ASN ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3974 GLN D4096 ASN ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 125860 Z= 0.368 Angle : 0.672 9.380 170648 Z= 0.345 Chirality : 0.042 0.378 19404 Planarity : 0.005 0.080 22256 Dihedral : 4.941 59.026 17678 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.25 % Allowed : 12.96 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.07), residues: 13424 helix: 0.57 (0.06), residues: 6576 sheet: -1.59 (0.13), residues: 1376 loop : -2.25 (0.08), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 557 HIS 0.021 0.002 HIS C 202 PHE 0.030 0.002 PHE D3853 TYR 0.024 0.002 TYR C4780 ARG 0.016 0.001 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 863 time to evaluate : 9.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.3864 (pp) REVERT: A 655 MET cc_start: 0.6902 (mmm) cc_final: 0.6660 (mmt) REVERT: A 1123 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: A 1174 MET cc_start: 0.7395 (mtp) cc_final: 0.6984 (mtm) REVERT: A 1951 ASN cc_start: 0.1893 (OUTLIER) cc_final: 0.0446 (m-40) REVERT: A 2003 MET cc_start: 0.8275 (mmm) cc_final: 0.7748 (mmt) REVERT: A 2233 MET cc_start: 0.7202 (pmm) cc_final: 0.6924 (pmm) REVERT: A 2781 MET cc_start: 0.1110 (ttp) cc_final: -0.0874 (mtt) REVERT: A 2843 MET cc_start: 0.0066 (tpp) cc_final: -0.0943 (ttp) REVERT: A 3853 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 4480 LYS cc_start: 0.5472 (mptt) cc_final: 0.4099 (mmmt) REVERT: A 4706 MET cc_start: 0.7239 (mmp) cc_final: 0.6969 (mmm) REVERT: B 117 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6799 (m170) REVERT: B 314 LEU cc_start: 0.4314 (OUTLIER) cc_final: 0.3815 (pp) REVERT: B 1174 MET cc_start: 0.7030 (mtp) cc_final: 0.6693 (mtm) REVERT: B 1288 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7016 (ptmm) REVERT: B 1295 ASN cc_start: 0.2333 (OUTLIER) cc_final: 0.2120 (m110) REVERT: B 1951 ASN cc_start: 0.2983 (OUTLIER) cc_final: 0.1276 (m-40) REVERT: B 2003 MET cc_start: 0.8213 (mmm) cc_final: 0.7612 (mmp) REVERT: B 2233 MET cc_start: 0.7598 (pmm) cc_final: 0.7242 (pmm) REVERT: B 2247 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7505 (ttp) REVERT: B 2278 MET cc_start: 0.7621 (mmt) cc_final: 0.7218 (tpt) REVERT: B 2385 ASN cc_start: 0.7033 (OUTLIER) cc_final: 0.6573 (t0) REVERT: B 2756 MET cc_start: -0.0006 (mmt) cc_final: -0.0239 (mmt) REVERT: B 2781 MET cc_start: 0.2004 (ttp) cc_final: 0.0010 (mtt) REVERT: B 2843 MET cc_start: 0.0135 (mmm) cc_final: -0.0178 (tmm) REVERT: B 3853 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8369 (t80) REVERT: B 4059 GLN cc_start: 0.5575 (tp40) cc_final: 0.5271 (tp-100) REVERT: B 4645 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7290 (p0) REVERT: B 4706 MET cc_start: 0.7327 (mmp) cc_final: 0.7048 (mmm) REVERT: H 14 ARG cc_start: 0.5434 (ttp-110) cc_final: 0.5017 (ttp-110) REVERT: C 241 MET cc_start: 0.1267 (OUTLIER) cc_final: 0.0818 (mtt) REVERT: C 314 LEU cc_start: 0.3648 (OUTLIER) cc_final: 0.3329 (pp) REVERT: C 655 MET cc_start: 0.6997 (mmm) cc_final: 0.6322 (mmt) REVERT: C 1174 MET cc_start: 0.7175 (mtp) cc_final: 0.6929 (mtm) REVERT: C 1215 MET cc_start: 0.6980 (tpp) cc_final: 0.6086 (tpp) REVERT: C 2003 MET cc_start: 0.8325 (mmm) cc_final: 0.7836 (mmp) REVERT: C 2352 ILE cc_start: 0.6781 (mm) cc_final: 0.6566 (mm) REVERT: C 2387 ILE cc_start: 0.8647 (mt) cc_final: 0.8372 (mt) REVERT: C 2428 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5853 (tp) REVERT: C 2756 MET cc_start: 0.2349 (mmt) cc_final: 0.1660 (mmt) REVERT: C 2781 MET cc_start: -0.1731 (ttp) cc_final: -0.2915 (mtt) REVERT: C 2842 MET cc_start: 0.1295 (mtt) cc_final: 0.0920 (mtm) REVERT: C 2843 MET cc_start: 0.1352 (tpt) cc_final: 0.1109 (tpp) REVERT: C 3853 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8267 (t80) REVERT: I 19 LYS cc_start: 0.7426 (tptt) cc_final: 0.7132 (tttp) REVERT: I 44 ASN cc_start: 0.8070 (m110) cc_final: 0.7763 (t0) REVERT: D 79 GLN cc_start: 0.5802 (pt0) cc_final: 0.5571 (pt0) REVERT: D 241 MET cc_start: 0.2209 (OUTLIER) cc_final: 0.1803 (mtp) REVERT: D 314 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3536 (pp) REVERT: D 655 MET cc_start: 0.7112 (mmm) cc_final: 0.6675 (mmt) REVERT: D 1174 MET cc_start: 0.7357 (mtp) cc_final: 0.6967 (mtm) REVERT: D 1695 MET cc_start: 0.7936 (mmt) cc_final: 0.7709 (mmt) REVERT: D 1772 ILE cc_start: 0.5984 (tp) cc_final: 0.5774 (mt) REVERT: D 1841 LYS cc_start: 0.8413 (mttt) cc_final: 0.7866 (ttmm) REVERT: D 1951 ASN cc_start: 0.2285 (OUTLIER) cc_final: 0.1438 (m-40) REVERT: D 2324 ILE cc_start: 0.6770 (pt) cc_final: 0.6544 (pt) REVERT: D 2756 MET cc_start: 0.0716 (mmt) cc_final: 0.0438 (mmt) REVERT: D 2781 MET cc_start: 0.1673 (ttp) cc_final: 0.1301 (ptp) REVERT: D 2843 MET cc_start: -0.0231 (OUTLIER) cc_final: -0.0583 (ttp) REVERT: D 3853 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8275 (t80) REVERT: D 3972 ASP cc_start: 0.7200 (t0) cc_final: 0.6948 (t0) REVERT: D 4645 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7218 (p0) REVERT: D 4706 MET cc_start: 0.7279 (mmp) cc_final: 0.6996 (mmm) outliers start: 265 outliers final: 164 residues processed: 1061 average time/residue: 0.9352 time to fit residues: 1787.3745 Evaluate side-chains 986 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 799 time to evaluate : 9.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1895 MET Chi-restraints excluded: chain A residue 1951 ASN Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3885 SER Chi-restraints excluded: chain A residue 3889 TRP Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4645 ASP Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1951 ASN Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2385 ASN Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3885 SER Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 4001 MET Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4288 SER Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4652 VAL Chi-restraints excluded: chain B residue 4663 ASP Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1730 MET Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1895 MET Chi-restraints excluded: chain D residue 1951 ASN Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2240 ASP Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2346 MET Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4288 SER Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1488 optimal weight: 20.0000 chunk 1132 optimal weight: 6.9990 chunk 781 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 718 optimal weight: 6.9990 chunk 1011 optimal weight: 7.9990 chunk 1511 optimal weight: 40.0000 chunk 1600 optimal weight: 20.0000 chunk 789 optimal weight: 9.9990 chunk 1432 optimal weight: 5.9990 chunk 431 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 GLN ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1969 GLN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN B1244 ASN ** B1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2480 GLN ** C2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3963 GLN ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 125860 Z= 0.297 Angle : 0.616 11.432 170648 Z= 0.315 Chirality : 0.040 0.300 19404 Planarity : 0.004 0.081 22256 Dihedral : 4.726 50.528 17666 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.67 % Allowed : 14.77 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.07), residues: 13424 helix: 0.72 (0.06), residues: 6588 sheet: -1.51 (0.14), residues: 1376 loop : -2.21 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D4644 HIS 0.018 0.001 HIS A1267 PHE 0.023 0.002 PHE C4845 TYR 0.020 0.002 TYR B4724 ARG 0.007 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 847 time to evaluate : 9.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.3691 (m90) cc_final: 0.3017 (m-70) REVERT: A 655 MET cc_start: 0.6805 (mmm) cc_final: 0.6563 (mmt) REVERT: A 1174 MET cc_start: 0.7392 (mtp) cc_final: 0.7060 (mtm) REVERT: A 1304 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7584 (mm) REVERT: A 2003 MET cc_start: 0.8292 (mmm) cc_final: 0.7609 (mmp) REVERT: A 2233 MET cc_start: 0.7342 (pmm) cc_final: 0.6870 (pmm) REVERT: A 2781 MET cc_start: 0.1262 (ttp) cc_final: -0.0909 (mtm) REVERT: A 2843 MET cc_start: 0.0071 (tpp) cc_final: -0.0791 (ttp) REVERT: A 3998 MET cc_start: 0.7807 (ttm) cc_final: 0.7597 (mtp) REVERT: A 4480 LYS cc_start: 0.5419 (mptt) cc_final: 0.4066 (mmmt) REVERT: A 4706 MET cc_start: 0.7192 (mmp) cc_final: 0.6923 (mmm) REVERT: G 44 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7929 (t0) REVERT: G 80 ASP cc_start: 0.7042 (p0) cc_final: 0.6737 (p0) REVERT: B 79 GLN cc_start: 0.5590 (pt0) cc_final: 0.5287 (pt0) REVERT: B 309 MET cc_start: 0.2862 (mtm) cc_final: 0.2649 (mtm) REVERT: B 314 LEU cc_start: 0.4238 (OUTLIER) cc_final: 0.3831 (pp) REVERT: B 995 MET cc_start: 0.2635 (mmm) cc_final: 0.1153 (mtp) REVERT: B 1168 MET cc_start: 0.7645 (mmt) cc_final: 0.7145 (mmm) REVERT: B 1174 MET cc_start: 0.7138 (mtp) cc_final: 0.6842 (mtm) REVERT: B 1668 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7535 (mm) REVERT: B 1952 MET cc_start: 0.2455 (tpp) cc_final: 0.2106 (tpt) REVERT: B 2003 MET cc_start: 0.8201 (mmm) cc_final: 0.7626 (mmp) REVERT: B 2233 MET cc_start: 0.7648 (pmm) cc_final: 0.7140 (pmm) REVERT: B 2278 MET cc_start: 0.7630 (mmt) cc_final: 0.7150 (tpt) REVERT: B 2358 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5060 (mmt180) REVERT: B 2756 MET cc_start: 0.0164 (mmt) cc_final: -0.0118 (mmt) REVERT: B 2781 MET cc_start: 0.2032 (ttp) cc_final: 0.0032 (mtt) REVERT: B 2843 MET cc_start: 0.0168 (mmm) cc_final: -0.0111 (tmm) REVERT: B 3818 MET cc_start: 0.3353 (tmm) cc_final: 0.2711 (tmm) REVERT: B 4706 MET cc_start: 0.7201 (mmp) cc_final: 0.6891 (mmm) REVERT: H 6 GLU cc_start: 0.7760 (tt0) cc_final: 0.7362 (mp0) REVERT: H 44 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (t0) REVERT: C 241 MET cc_start: 0.1302 (OUTLIER) cc_final: 0.0845 (mtt) REVERT: C 655 MET cc_start: 0.6899 (mmm) cc_final: 0.6403 (mmt) REVERT: C 940 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.4101 (mp) REVERT: C 995 MET cc_start: 0.3177 (mmm) cc_final: 0.1688 (mtp) REVERT: C 1174 MET cc_start: 0.6697 (mtp) cc_final: 0.6434 (mtm) REVERT: C 1215 MET cc_start: 0.6899 (tpp) cc_final: 0.6654 (tpp) REVERT: C 1668 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 1975 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7226 (pp) REVERT: C 2003 MET cc_start: 0.8312 (mmm) cc_final: 0.7845 (mmp) REVERT: C 2149 MET cc_start: 0.8136 (mmt) cc_final: 0.7904 (mmt) REVERT: C 2358 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.4871 (mmt180) REVERT: C 2387 ILE cc_start: 0.8557 (mt) cc_final: 0.8317 (mt) REVERT: C 2756 MET cc_start: 0.2426 (mmt) cc_final: 0.1883 (mmt) REVERT: C 2781 MET cc_start: -0.2230 (ttp) cc_final: -0.3366 (mtt) REVERT: I 19 LYS cc_start: 0.7644 (tptt) cc_final: 0.7344 (tttp) REVERT: I 44 ASN cc_start: 0.8100 (m110) cc_final: 0.7806 (t0) REVERT: D 241 MET cc_start: 0.2139 (OUTLIER) cc_final: 0.1765 (mtp) REVERT: D 314 LEU cc_start: 0.4157 (OUTLIER) cc_final: 0.3691 (pp) REVERT: D 655 MET cc_start: 0.7064 (mmm) cc_final: 0.6666 (mmt) REVERT: D 1174 MET cc_start: 0.7280 (mtp) cc_final: 0.6896 (mtm) REVERT: D 1304 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7636 (mm) REVERT: D 1841 LYS cc_start: 0.8412 (mttt) cc_final: 0.7878 (ttmm) REVERT: D 1952 MET cc_start: 0.3781 (tpp) cc_final: 0.3083 (tpt) REVERT: D 2278 MET cc_start: 0.7385 (mmt) cc_final: 0.7117 (tpt) REVERT: D 2324 ILE cc_start: 0.7041 (pt) cc_final: 0.6832 (pt) REVERT: D 2388 MET cc_start: 0.7814 (mtt) cc_final: 0.7568 (mtt) REVERT: D 2428 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6143 (tt) REVERT: D 2756 MET cc_start: 0.0359 (mmt) cc_final: 0.0112 (mmt) REVERT: D 2781 MET cc_start: 0.1581 (ttp) cc_final: 0.1201 (ptp) REVERT: D 2843 MET cc_start: -0.0141 (OUTLIER) cc_final: -0.0633 (ttp) REVERT: D 2891 ILE cc_start: 0.1560 (OUTLIER) cc_final: 0.1029 (mt) REVERT: D 4698 ASN cc_start: 0.3805 (OUTLIER) cc_final: 0.3480 (p0) REVERT: J 6 GLU cc_start: 0.7481 (tt0) cc_final: 0.7241 (mp0) outliers start: 315 outliers final: 200 residues processed: 1094 average time/residue: 0.9340 time to fit residues: 1846.9142 Evaluate side-chains 1021 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 803 time to evaluate : 9.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3885 SER Chi-restraints excluded: chain A residue 3889 TRP Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 2128 LEU Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2358 ARG Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3885 SER Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4288 SER Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4632 LEU Chi-restraints excluded: chain B residue 4663 ASP Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1792 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2358 ARG Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3724 LEU Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4288 SER Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1895 MET Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2240 ASP Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3930 ASN Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4288 SER Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1333 optimal weight: 0.4980 chunk 908 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 1191 optimal weight: 1.9990 chunk 660 optimal weight: 3.9990 chunk 1365 optimal weight: 30.0000 chunk 1106 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 817 optimal weight: 2.9990 chunk 1436 optimal weight: 5.9990 chunk 403 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 HIS A1244 ASN ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS C1244 ASN C1627 GLN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 HIS D1244 ASN ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2194 ASN D3633 HIS ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3954 GLN ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 125860 Z= 0.186 Angle : 0.548 10.878 170648 Z= 0.281 Chirality : 0.037 0.216 19404 Planarity : 0.004 0.085 22256 Dihedral : 4.433 41.745 17666 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.49 % Allowed : 15.74 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.07), residues: 13424 helix: 1.00 (0.07), residues: 6592 sheet: -1.38 (0.14), residues: 1372 loop : -2.13 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4644 HIS 0.029 0.001 HIS A1267 PHE 0.016 0.001 PHE A4845 TYR 0.014 0.001 TYR A3690 ARG 0.006 0.000 ARG C4842 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 866 time to evaluate : 9.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.3925 (m90) cc_final: 0.3408 (m-70) REVERT: A 655 MET cc_start: 0.6963 (mmm) cc_final: 0.6622 (mmt) REVERT: A 1174 MET cc_start: 0.7342 (mtp) cc_final: 0.7002 (mtm) REVERT: A 1841 LYS cc_start: 0.8324 (mttt) cc_final: 0.7882 (ttmm) REVERT: A 2003 MET cc_start: 0.8268 (mmm) cc_final: 0.7652 (mmp) REVERT: A 2233 MET cc_start: 0.7446 (pmm) cc_final: 0.6959 (pmm) REVERT: A 2358 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.4827 (mmt180) REVERT: A 2459 PHE cc_start: 0.6586 (t80) cc_final: 0.6381 (t80) REVERT: A 2781 MET cc_start: 0.1274 (ttp) cc_final: -0.1046 (mtt) REVERT: A 2843 MET cc_start: 0.0049 (tpp) cc_final: -0.0813 (ttp) REVERT: A 4034 TYR cc_start: 0.4445 (OUTLIER) cc_final: 0.2822 (m-80) REVERT: A 4480 LYS cc_start: 0.5255 (mptt) cc_final: 0.3976 (mmmt) REVERT: B 79 GLN cc_start: 0.5498 (pt0) cc_final: 0.5213 (pt0) REVERT: B 309 MET cc_start: 0.2832 (mtm) cc_final: 0.2614 (mtm) REVERT: B 995 MET cc_start: 0.2569 (mmm) cc_final: 0.1146 (mtp) REVERT: B 1168 MET cc_start: 0.7606 (mmt) cc_final: 0.7130 (mmm) REVERT: B 1288 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6966 (ptmm) REVERT: B 1364 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6131 (pp20) REVERT: B 1952 MET cc_start: 0.2752 (tpp) cc_final: 0.2470 (tpt) REVERT: B 2003 MET cc_start: 0.8196 (mmm) cc_final: 0.7647 (mmp) REVERT: B 2233 MET cc_start: 0.7613 (pmm) cc_final: 0.7004 (pmm) REVERT: B 2247 MET cc_start: 0.7799 (tpp) cc_final: 0.7368 (ttp) REVERT: B 2278 MET cc_start: 0.7597 (mmt) cc_final: 0.7103 (tpt) REVERT: B 2388 MET cc_start: 0.7885 (mtt) cc_final: 0.7628 (mtt) REVERT: B 2459 PHE cc_start: 0.6638 (t80) cc_final: 0.6128 (t80) REVERT: B 2756 MET cc_start: 0.0114 (mmt) cc_final: -0.0115 (mmt) REVERT: B 2781 MET cc_start: 0.2045 (ttp) cc_final: 0.0031 (mtt) REVERT: B 2843 MET cc_start: 0.0335 (mmm) cc_final: -0.0580 (tmm) REVERT: B 3818 MET cc_start: 0.3408 (tmm) cc_final: 0.2525 (tmm) REVERT: B 3853 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8330 (t80) REVERT: B 4051 MET cc_start: 0.5392 (mtp) cc_final: 0.5174 (ttm) REVERT: B 4280 LEU cc_start: 0.7074 (mt) cc_final: 0.6868 (mt) REVERT: B 4480 LYS cc_start: 0.5198 (mptt) cc_final: 0.4075 (mmmt) REVERT: B 4490 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 4645 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7087 (p0) REVERT: H 6 GLU cc_start: 0.7693 (tt0) cc_final: 0.7150 (mp0) REVERT: C 241 MET cc_start: 0.1242 (OUTLIER) cc_final: 0.0811 (mtt) REVERT: C 494 MET cc_start: 0.6888 (tpp) cc_final: 0.6508 (mmm) REVERT: C 655 MET cc_start: 0.6900 (mmm) cc_final: 0.6546 (mmt) REVERT: C 940 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3968 (mp) REVERT: C 995 MET cc_start: 0.3286 (mmm) cc_final: 0.1738 (mtp) REVERT: C 1975 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7165 (pp) REVERT: C 2003 MET cc_start: 0.8275 (mmm) cc_final: 0.7810 (mmp) REVERT: C 2352 ILE cc_start: 0.6620 (mm) cc_final: 0.6172 (mm) REVERT: C 2387 ILE cc_start: 0.8550 (mt) cc_final: 0.8317 (mt) REVERT: C 2428 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5888 (tp) REVERT: C 2756 MET cc_start: 0.2378 (mmt) cc_final: 0.1886 (mmt) REVERT: C 2781 MET cc_start: -0.2158 (ttp) cc_final: -0.3142 (mtt) REVERT: C 2842 MET cc_start: 0.1319 (mpp) cc_final: 0.0082 (mmm) REVERT: C 4034 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.2829 (m-80) REVERT: C 4480 LYS cc_start: 0.5658 (mptt) cc_final: 0.4306 (mmmt) REVERT: I 44 ASN cc_start: 0.8027 (m110) cc_final: 0.7795 (t0) REVERT: D 655 MET cc_start: 0.7310 (mmm) cc_final: 0.6812 (mmt) REVERT: D 995 MET cc_start: 0.2739 (mmm) cc_final: 0.1404 (mtp) REVERT: D 1174 MET cc_start: 0.7218 (mtp) cc_final: 0.6850 (mtm) REVERT: D 2003 MET cc_start: 0.8206 (mmm) cc_final: 0.7539 (mmp) REVERT: D 2247 MET cc_start: 0.7784 (tpp) cc_final: 0.7226 (ttp) REVERT: D 2278 MET cc_start: 0.7343 (mmt) cc_final: 0.6997 (tpt) REVERT: D 2324 ILE cc_start: 0.6970 (pt) cc_final: 0.6767 (pt) REVERT: D 2428 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6110 (tt) REVERT: D 2781 MET cc_start: 0.1549 (ttp) cc_final: 0.1188 (ptp) REVERT: D 2843 MET cc_start: -0.0330 (OUTLIER) cc_final: -0.0749 (ttp) REVERT: D 2891 ILE cc_start: 0.1476 (OUTLIER) cc_final: 0.0923 (mt) REVERT: D 3853 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8249 (t80) REVERT: D 4645 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7127 (p0) REVERT: J 6 GLU cc_start: 0.7431 (tt0) cc_final: 0.7230 (mp0) outliers start: 294 outliers final: 189 residues processed: 1093 average time/residue: 0.9619 time to fit residues: 1891.2724 Evaluate side-chains 1030 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 824 time to evaluate : 9.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3885 SER Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4490 LEU Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3805 ASN Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 4034 TYR Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 538 optimal weight: 6.9990 chunk 1441 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 939 optimal weight: 9.9990 chunk 395 optimal weight: 8.9990 chunk 1602 optimal weight: 8.9990 chunk 1330 optimal weight: 0.0040 chunk 741 optimal weight: 6.9990 chunk 133 optimal weight: 40.0000 chunk 530 optimal weight: 10.0000 chunk 841 optimal weight: 0.4980 overall best weight: 4.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 ASN A1123 GLN ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2728 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS B 692 HIS B1046 ASN ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2728 HIS ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2728 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 193 HIS ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1711 HIS ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3948 HIS D3954 GLN D3974 GLN ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 125860 Z= 0.316 Angle : 0.634 12.052 170648 Z= 0.324 Chirality : 0.040 0.202 19404 Planarity : 0.005 0.078 22256 Dihedral : 4.653 32.360 17663 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.34 % Allowed : 15.85 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.07), residues: 13424 helix: 0.82 (0.06), residues: 6596 sheet: -1.42 (0.14), residues: 1372 loop : -2.15 (0.08), residues: 5456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C4644 HIS 0.030 0.001 HIS D1267 PHE 0.025 0.002 PHE C4845 TYR 0.022 0.002 TYR B4724 ARG 0.009 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 832 time to evaluate : 9.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.6498 (pp) cc_final: 0.6184 (mt) REVERT: A 995 MET cc_start: 0.2824 (mmm) cc_final: 0.1350 (mtp) REVERT: A 1174 MET cc_start: 0.7371 (mtp) cc_final: 0.6991 (mtm) REVERT: A 1364 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.5892 (pp20) REVERT: A 2003 MET cc_start: 0.8283 (mmm) cc_final: 0.7718 (mmp) REVERT: A 2233 MET cc_start: 0.7467 (pmm) cc_final: 0.6880 (pmm) REVERT: A 2262 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 2277 GLN cc_start: 0.7184 (mp-120) cc_final: 0.6761 (mm110) REVERT: A 2278 MET cc_start: 0.7245 (mmt) cc_final: 0.6990 (tpt) REVERT: A 2358 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.4945 (mmt180) REVERT: A 2459 PHE cc_start: 0.6754 (t80) cc_final: 0.6519 (t80) REVERT: A 2781 MET cc_start: 0.0947 (ttp) cc_final: -0.0927 (mtm) REVERT: A 2843 MET cc_start: -0.0259 (tpp) cc_final: -0.1181 (ttp) REVERT: A 3818 MET cc_start: 0.3070 (tmm) cc_final: 0.2725 (tmm) REVERT: A 3853 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8226 (t80) REVERT: A 4480 LYS cc_start: 0.5004 (mptt) cc_final: 0.3870 (mmmt) REVERT: B 309 MET cc_start: 0.3058 (OUTLIER) cc_final: 0.2827 (mtm) REVERT: B 314 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3805 (pp) REVERT: B 995 MET cc_start: 0.2846 (mmm) cc_final: 0.1611 (mtp) REVERT: B 1168 MET cc_start: 0.7077 (mmt) cc_final: 0.6819 (mmm) REVERT: B 1288 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6958 (ptmm) REVERT: B 1364 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5917 (pp20) REVERT: B 1952 MET cc_start: 0.2241 (tpp) cc_final: 0.2000 (tpt) REVERT: B 2003 MET cc_start: 0.8282 (mmm) cc_final: 0.7899 (mmp) REVERT: B 2247 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7524 (ttp) REVERT: B 2358 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5050 (mmt180) REVERT: B 2756 MET cc_start: 0.0220 (mmt) cc_final: -0.0027 (mmt) REVERT: B 2781 MET cc_start: 0.2129 (ttp) cc_final: 0.0197 (mtt) REVERT: B 2843 MET cc_start: 0.0598 (mmm) cc_final: -0.0506 (tmm) REVERT: B 3818 MET cc_start: 0.3552 (tmm) cc_final: 0.2435 (tmm) REVERT: B 3853 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8292 (t80) REVERT: B 4051 MET cc_start: 0.5655 (mtp) cc_final: 0.5216 (ttm) REVERT: B 4119 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6530 (mm-30) REVERT: B 4490 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8504 (mt) REVERT: H 6 GLU cc_start: 0.7774 (tt0) cc_final: 0.7178 (mp0) REVERT: C 241 MET cc_start: 0.1365 (OUTLIER) cc_final: 0.0947 (mtt) REVERT: C 655 MET cc_start: 0.6968 (mmm) cc_final: 0.6475 (mmt) REVERT: C 940 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3763 (mp) REVERT: C 995 MET cc_start: 0.2792 (mmm) cc_final: 0.1430 (mtp) REVERT: C 1364 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5145 (pp20) REVERT: C 2003 MET cc_start: 0.8318 (mmm) cc_final: 0.7865 (mmp) REVERT: C 2387 ILE cc_start: 0.8758 (mt) cc_final: 0.8528 (mt) REVERT: C 2756 MET cc_start: 0.1405 (mmt) cc_final: 0.1078 (mmt) REVERT: C 2781 MET cc_start: -0.2153 (ttp) cc_final: -0.3109 (mtt) REVERT: C 3818 MET cc_start: 0.2980 (tmm) cc_final: 0.2569 (tmm) REVERT: C 3853 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8184 (t80) REVERT: C 4480 LYS cc_start: 0.5810 (mptt) cc_final: 0.4403 (mmmt) REVERT: C 4490 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8466 (mt) REVERT: I 31 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8076 (mt) REVERT: I 44 ASN cc_start: 0.8128 (m110) cc_final: 0.7849 (t0) REVERT: D 314 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3792 (pp) REVERT: D 655 MET cc_start: 0.7025 (mmm) cc_final: 0.6550 (mmt) REVERT: D 995 MET cc_start: 0.2526 (mmm) cc_final: 0.1890 (mmm) REVERT: D 1174 MET cc_start: 0.7155 (mtp) cc_final: 0.6739 (mtm) REVERT: D 1364 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6184 (pp20) REVERT: D 2003 MET cc_start: 0.8300 (mmm) cc_final: 0.7649 (mmp) REVERT: D 2247 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7528 (ttp) REVERT: D 2358 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5018 (mmt180) REVERT: D 2428 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6133 (tt) REVERT: D 2756 MET cc_start: 0.1470 (mmt) cc_final: 0.1089 (mmt) REVERT: D 2781 MET cc_start: 0.1578 (ttp) cc_final: 0.1202 (ptp) REVERT: D 2843 MET cc_start: -0.0040 (OUTLIER) cc_final: -0.0351 (ttt) REVERT: D 2891 ILE cc_start: 0.1464 (OUTLIER) cc_final: 0.1069 (mt) REVERT: D 3853 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8175 (t80) REVERT: D 4698 ASN cc_start: 0.3967 (OUTLIER) cc_final: 0.3625 (p0) outliers start: 394 outliers final: 264 residues processed: 1163 average time/residue: 0.9529 time to fit residues: 2007.6458 Evaluate side-chains 1091 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 800 time to evaluate : 9.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2262 GLU Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4632 LEU Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1792 THR Chi-restraints excluded: chain B residue 1806 HIS Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1978 PHE Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2358 ARG Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4018 MET Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4490 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4632 LEU Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4652 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1221 VAL Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1743 GLU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2262 GLU Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3724 LEU Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3884 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4490 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4632 LEU Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2240 ASP Chi-restraints excluded: chain D residue 2247 MET Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2358 ARG Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3885 SER Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1544 optimal weight: 0.3980 chunk 180 optimal weight: 10.0000 chunk 912 optimal weight: 8.9990 chunk 1170 optimal weight: 2.9990 chunk 906 optimal weight: 0.0870 chunk 1348 optimal weight: 20.0000 chunk 894 optimal weight: 30.0000 chunk 1596 optimal weight: 5.9990 chunk 998 optimal weight: 10.0000 chunk 973 optimal weight: 8.9990 chunk 736 optimal weight: 1.9990 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3633 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2385 ASN ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2151 ASN ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 125860 Z= 0.192 Angle : 0.558 12.722 170648 Z= 0.286 Chirality : 0.037 0.183 19404 Planarity : 0.004 0.087 22256 Dihedral : 4.416 28.950 17662 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.95 % Allowed : 16.86 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.07), residues: 13424 helix: 1.05 (0.07), residues: 6580 sheet: -1.35 (0.14), residues: 1372 loop : -2.09 (0.08), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D4644 HIS 0.029 0.001 HIS C1267 PHE 0.017 0.001 PHE B4659 TYR 0.014 0.001 TYR B1777 ARG 0.008 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 840 time to evaluate : 9.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.6514 (pp) cc_final: 0.6177 (mt) REVERT: A 995 MET cc_start: 0.2836 (mmm) cc_final: 0.1263 (mtp) REVERT: A 1174 MET cc_start: 0.7247 (mtp) cc_final: 0.6888 (mtm) REVERT: A 1364 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5910 (pp20) REVERT: A 2003 MET cc_start: 0.8305 (mmm) cc_final: 0.7763 (mmp) REVERT: A 2262 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: A 2278 MET cc_start: 0.7248 (mmt) cc_final: 0.7013 (tpt) REVERT: A 2358 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.4942 (mmt180) REVERT: A 2781 MET cc_start: 0.0953 (ttp) cc_final: -0.0937 (mtm) REVERT: A 2843 MET cc_start: -0.0304 (tpp) cc_final: -0.1168 (ttp) REVERT: A 3818 MET cc_start: 0.2571 (tmm) cc_final: 0.2277 (tmm) REVERT: A 3853 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8281 (t80) REVERT: A 4034 TYR cc_start: 0.4285 (OUTLIER) cc_final: 0.3330 (m-80) REVERT: A 4480 LYS cc_start: 0.5291 (mptt) cc_final: 0.4085 (mmmt) REVERT: B 995 MET cc_start: 0.2777 (mmm) cc_final: 0.1598 (mtp) REVERT: B 1168 MET cc_start: 0.7049 (mmt) cc_final: 0.6828 (mmm) REVERT: B 1288 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6953 (ptmm) REVERT: B 1364 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6114 (pp20) REVERT: B 1960 LYS cc_start: 0.4279 (OUTLIER) cc_final: 0.4015 (mmtm) REVERT: B 2003 MET cc_start: 0.8189 (mmm) cc_final: 0.7611 (mmp) REVERT: B 2236 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7144 (p) REVERT: B 2247 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7480 (ttp) REVERT: B 2262 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: B 2459 PHE cc_start: 0.6802 (t80) cc_final: 0.6466 (t80) REVERT: B 2756 MET cc_start: 0.0178 (mmt) cc_final: -0.0103 (mmt) REVERT: B 2781 MET cc_start: 0.2142 (ttp) cc_final: 0.0208 (mtt) REVERT: B 2843 MET cc_start: 0.0665 (mmm) cc_final: -0.0378 (tmm) REVERT: B 3818 MET cc_start: 0.3459 (tmm) cc_final: 0.2400 (tmm) REVERT: B 3853 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8322 (t80) REVERT: B 4034 TYR cc_start: 0.4111 (OUTLIER) cc_final: 0.3067 (m-80) REVERT: B 4051 MET cc_start: 0.5511 (mtp) cc_final: 0.5248 (ttm) REVERT: B 4645 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7252 (p0) REVERT: C 241 MET cc_start: 0.1317 (OUTLIER) cc_final: 0.0921 (mtt) REVERT: C 655 MET cc_start: 0.6924 (mmm) cc_final: 0.6537 (mmt) REVERT: C 940 LEU cc_start: 0.3859 (OUTLIER) cc_final: 0.3578 (mp) REVERT: C 995 MET cc_start: 0.2890 (mmm) cc_final: 0.1475 (mtp) REVERT: C 1364 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5097 (pp20) REVERT: C 2003 MET cc_start: 0.8297 (mmm) cc_final: 0.7839 (mmp) REVERT: C 2358 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5192 (mmm160) REVERT: C 2385 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6741 (t0) REVERT: C 2428 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.6004 (tp) REVERT: C 2506 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6307 (tt) REVERT: C 2756 MET cc_start: 0.1333 (mmt) cc_final: 0.1056 (mmt) REVERT: C 2781 MET cc_start: -0.2252 (ttp) cc_final: -0.3234 (mtt) REVERT: C 2842 MET cc_start: 0.1570 (mpp) cc_final: -0.0195 (mmm) REVERT: C 3818 MET cc_start: 0.2743 (tmm) cc_final: 0.2153 (tmm) REVERT: C 3853 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8248 (t80) REVERT: C 4034 TYR cc_start: 0.4364 (OUTLIER) cc_final: 0.3355 (m-80) REVERT: C 4480 LYS cc_start: 0.5736 (mptt) cc_final: 0.4403 (mmmt) REVERT: I 44 ASN cc_start: 0.8053 (m110) cc_final: 0.7803 (t0) REVERT: I 69 LEU cc_start: 0.7816 (tt) cc_final: 0.7580 (tt) REVERT: D 314 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.3863 (pp) REVERT: D 655 MET cc_start: 0.7142 (mmm) cc_final: 0.6417 (mmt) REVERT: D 995 MET cc_start: 0.2822 (mmm) cc_final: 0.1475 (mtp) REVERT: D 1174 MET cc_start: 0.7230 (mtp) cc_final: 0.6851 (mtm) REVERT: D 1364 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6200 (pp20) REVERT: D 2003 MET cc_start: 0.8251 (mmm) cc_final: 0.7585 (mmp) REVERT: D 2247 MET cc_start: 0.7855 (tpp) cc_final: 0.7420 (ttp) REVERT: D 2358 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5008 (mmt180) REVERT: D 2428 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6096 (tt) REVERT: D 2756 MET cc_start: 0.0513 (mmt) cc_final: 0.0145 (mmt) REVERT: D 2781 MET cc_start: 0.1561 (ttp) cc_final: 0.1199 (ptp) REVERT: D 2843 MET cc_start: -0.0181 (OUTLIER) cc_final: -0.0698 (ttp) REVERT: D 2891 ILE cc_start: 0.1535 (OUTLIER) cc_final: 0.1036 (mt) REVERT: D 3853 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8231 (t80) REVERT: D 4698 ASN cc_start: 0.3906 (OUTLIER) cc_final: 0.3550 (p0) outliers start: 348 outliers final: 242 residues processed: 1120 average time/residue: 1.0344 time to fit residues: 2099.2048 Evaluate side-chains 1089 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 816 time to evaluate : 9.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2262 GLU Chi-restraints excluded: chain A residue 2335 ARG Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1806 HIS Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1960 LYS Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2236 SER Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2262 GLU Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2357 SER Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4034 TYR Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4509 PHE Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1365 THR Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2262 GLU Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2358 ARG Chi-restraints excluded: chain C residue 2385 ASN Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4034 TYR Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4288 SER Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2358 ARG Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4500 MET Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 987 optimal weight: 9.9990 chunk 637 optimal weight: 40.0000 chunk 953 optimal weight: 20.0000 chunk 480 optimal weight: 20.0000 chunk 313 optimal weight: 0.7980 chunk 309 optimal weight: 8.9990 chunk 1014 optimal weight: 9.9990 chunk 1087 optimal weight: 50.0000 chunk 789 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 1254 optimal weight: 3.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1837 ASN ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2480 GLN B2848 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 ASN ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3963 GLN ** C4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 ASN ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2848 HIS ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 125860 Z= 0.329 Angle : 0.648 14.199 170648 Z= 0.329 Chirality : 0.040 0.246 19404 Planarity : 0.005 0.088 22256 Dihedral : 4.666 28.147 17658 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.28 % Allowed : 16.91 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.07), residues: 13424 helix: 0.83 (0.06), residues: 6580 sheet: -1.40 (0.14), residues: 1364 loop : -2.16 (0.08), residues: 5480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A4644 HIS 0.017 0.001 HIS C1267 PHE 0.029 0.002 PHE A1137 TYR 0.023 0.002 TYR C4724 ARG 0.008 0.001 ARG B1719 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 813 time to evaluate : 8.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: A 995 MET cc_start: 0.2548 (mmm) cc_final: 0.1904 (mmm) REVERT: A 1174 MET cc_start: 0.7271 (mtp) cc_final: 0.6871 (mtm) REVERT: A 1364 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6093 (pp20) REVERT: A 2003 MET cc_start: 0.8343 (mmm) cc_final: 0.7836 (mmp) REVERT: A 2262 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 2278 MET cc_start: 0.7329 (mmt) cc_final: 0.6992 (tpt) REVERT: A 2358 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.4994 (mmt180) REVERT: A 2781 MET cc_start: 0.1213 (ttp) cc_final: -0.0770 (mtt) REVERT: A 2843 MET cc_start: -0.0028 (tpp) cc_final: -0.0980 (ttp) REVERT: A 3818 MET cc_start: 0.3353 (tmm) cc_final: 0.2966 (tmm) REVERT: A 3853 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8213 (t80) REVERT: A 4480 LYS cc_start: 0.5022 (mptt) cc_final: 0.3887 (mmmt) REVERT: A 4706 MET cc_start: 0.7046 (ttt) cc_final: 0.6787 (ttm) REVERT: G 31 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 995 MET cc_start: 0.3099 (mmm) cc_final: 0.1685 (mtp) REVERT: B 1168 MET cc_start: 0.7101 (mmt) cc_final: 0.6860 (mmm) REVERT: B 1288 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6925 (ptmm) REVERT: B 1364 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6000 (pp20) REVERT: B 2003 MET cc_start: 0.8254 (mmm) cc_final: 0.7722 (mmp) REVERT: B 2247 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7561 (ttp) REVERT: B 2358 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5064 (mmt180) REVERT: B 2459 PHE cc_start: 0.6975 (t80) cc_final: 0.6595 (t80) REVERT: B 2756 MET cc_start: 0.0278 (mmt) cc_final: -0.0016 (mmt) REVERT: B 2781 MET cc_start: 0.2145 (ttp) cc_final: 0.0243 (mtt) REVERT: B 2839 MET cc_start: -0.0930 (ttp) cc_final: -0.1939 (mtt) REVERT: B 2843 MET cc_start: 0.0542 (mmm) cc_final: -0.0621 (tmm) REVERT: B 3818 MET cc_start: 0.3460 (tmm) cc_final: 0.2404 (tmm) REVERT: B 3853 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8295 (t80) REVERT: B 4051 MET cc_start: 0.5552 (mtp) cc_final: 0.5298 (ttm) REVERT: C 241 MET cc_start: 0.1347 (OUTLIER) cc_final: 0.0944 (mtt) REVERT: C 655 MET cc_start: 0.6952 (mmm) cc_final: 0.6558 (mmt) REVERT: C 940 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3653 (mp) REVERT: C 995 MET cc_start: 0.3231 (mmm) cc_final: 0.1795 (mtp) REVERT: C 1364 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5200 (pp20) REVERT: C 2003 MET cc_start: 0.8385 (mmm) cc_final: 0.7934 (mmp) REVERT: C 2335 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6007 (tmm160) REVERT: C 2358 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.4423 (mmm160) REVERT: C 2756 MET cc_start: 0.1654 (mmt) cc_final: 0.1286 (mmt) REVERT: C 2781 MET cc_start: -0.2241 (ttp) cc_final: -0.3202 (mtt) REVERT: C 3818 MET cc_start: 0.3307 (tmm) cc_final: 0.2336 (tmm) REVERT: C 3853 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8163 (t80) REVERT: I 31 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8087 (mt) REVERT: I 44 ASN cc_start: 0.8099 (m110) cc_final: 0.7857 (t0) REVERT: I 104 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8016 (tp) REVERT: D 314 LEU cc_start: 0.4135 (OUTLIER) cc_final: 0.3657 (pp) REVERT: D 655 MET cc_start: 0.7261 (mmm) cc_final: 0.6706 (mmt) REVERT: D 995 MET cc_start: 0.2357 (mmm) cc_final: 0.1657 (mmm) REVERT: D 1174 MET cc_start: 0.7243 (mtp) cc_final: 0.6818 (mtm) REVERT: D 1364 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6322 (pp20) REVERT: D 2003 MET cc_start: 0.8342 (mmm) cc_final: 0.7759 (mmp) REVERT: D 2247 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7642 (ttp) REVERT: D 2358 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5058 (mmt180) REVERT: D 2428 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6066 (tt) REVERT: D 2756 MET cc_start: 0.0808 (mmt) cc_final: 0.0333 (mmt) REVERT: D 2781 MET cc_start: 0.1603 (ttp) cc_final: 0.1228 (ptp) REVERT: D 2843 MET cc_start: 0.0004 (OUTLIER) cc_final: -0.0263 (ttt) REVERT: D 2891 ILE cc_start: 0.1556 (OUTLIER) cc_final: 0.1156 (mt) REVERT: D 3853 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 4698 ASN cc_start: 0.4035 (OUTLIER) cc_final: 0.3673 (p0) REVERT: D 4706 MET cc_start: 0.7058 (ttt) cc_final: 0.6823 (ttm) REVERT: J 31 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8082 (mt) outliers start: 387 outliers final: 284 residues processed: 1139 average time/residue: 0.9258 time to fit residues: 1910.5936 Evaluate side-chains 1108 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 795 time to evaluate : 9.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2262 GLU Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2335 ARG Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2389 THR Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1806 HIS Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1978 PHE Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2262 GLU Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2358 ARG Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4632 LEU Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4652 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1169 ASN Chi-restraints excluded: chain C residue 1185 ASP Chi-restraints excluded: chain C residue 1221 VAL Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1365 THR Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1743 GLU Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2094 ILE Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2233 MET Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2262 GLU Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2358 ARG Chi-restraints excluded: chain C residue 2389 THR Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2902 VAL Chi-restraints excluded: chain C residue 3617 ASN Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3724 LEU Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3884 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4288 SER Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4632 LEU Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1261 VAL Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1792 THR Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2240 ASP Chi-restraints excluded: chain D residue 2247 MET Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2262 GLU Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2358 ARG Chi-restraints excluded: chain D residue 2389 THR Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 2891 ILE Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3889 TRP Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4288 SER Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1451 optimal weight: 9.9990 chunk 1529 optimal weight: 40.0000 chunk 1395 optimal weight: 10.0000 chunk 1487 optimal weight: 20.0000 chunk 1528 optimal weight: 30.0000 chunk 895 optimal weight: 0.6980 chunk 647 optimal weight: 1.9990 chunk 1167 optimal weight: 0.9990 chunk 456 optimal weight: 6.9990 chunk 1344 optimal weight: 20.0000 chunk 1406 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2151 ASN ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1969 GLN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1744 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 125860 Z= 0.198 Angle : 0.566 12.737 170648 Z= 0.288 Chirality : 0.038 0.280 19404 Planarity : 0.004 0.094 22256 Dihedral : 4.419 29.663 17658 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.81 % Allowed : 17.34 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.07), residues: 13424 helix: 1.05 (0.07), residues: 6580 sheet: -1.33 (0.14), residues: 1364 loop : -2.09 (0.08), residues: 5480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D4644 HIS 0.036 0.001 HIS A1267 PHE 0.025 0.001 PHE A1137 TYR 0.014 0.001 TYR B2723 ARG 0.008 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 835 time to evaluate : 9.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.2603 (mmm) cc_final: 0.1958 (mmm) REVERT: A 1174 MET cc_start: 0.7178 (mtp) cc_final: 0.6780 (mtm) REVERT: A 1364 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6116 (pp20) REVERT: A 1615 ARG cc_start: 0.4016 (mmp-170) cc_final: 0.3590 (mmm160) REVERT: A 1960 LYS cc_start: 0.4925 (OUTLIER) cc_final: 0.4641 (mmtm) REVERT: A 2003 MET cc_start: 0.8310 (mmm) cc_final: 0.7793 (mmp) REVERT: A 2262 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: A 2278 MET cc_start: 0.7316 (mmt) cc_final: 0.7009 (tpt) REVERT: A 2358 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.4996 (mmt180) REVERT: A 2428 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5738 (tp) REVERT: A 2459 PHE cc_start: 0.6813 (t80) cc_final: 0.6610 (t80) REVERT: A 2781 MET cc_start: 0.1220 (ttp) cc_final: -0.0687 (mtm) REVERT: A 2843 MET cc_start: -0.0262 (tpp) cc_final: -0.1112 (ttp) REVERT: A 3818 MET cc_start: 0.3114 (tmm) cc_final: 0.2749 (tmm) REVERT: A 3853 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 4480 LYS cc_start: 0.5300 (mptt) cc_final: 0.4100 (mmmt) REVERT: A 4490 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 4706 MET cc_start: 0.7005 (ttt) cc_final: 0.6783 (ttm) REVERT: B 995 MET cc_start: 0.3050 (mmm) cc_final: 0.1672 (mtp) REVERT: B 1288 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6858 (ptmm) REVERT: B 1364 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6123 (pp20) REVERT: B 2003 MET cc_start: 0.8194 (mmm) cc_final: 0.7617 (mmp) REVERT: B 2247 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7529 (ttp) REVERT: B 2262 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: B 2756 MET cc_start: 0.0227 (mmt) cc_final: 0.0010 (mmt) REVERT: B 2781 MET cc_start: 0.2143 (ttp) cc_final: 0.0222 (mtt) REVERT: B 2839 MET cc_start: -0.0723 (ttp) cc_final: -0.1784 (mtt) REVERT: B 2843 MET cc_start: 0.0362 (mmm) cc_final: -0.0694 (tmm) REVERT: B 3818 MET cc_start: 0.3386 (tmm) cc_final: 0.2219 (tmm) REVERT: B 3853 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 4051 MET cc_start: 0.5477 (mtp) cc_final: 0.5234 (ttm) REVERT: B 4480 LYS cc_start: 0.5183 (mptt) cc_final: 0.4107 (mmmt) REVERT: B 4490 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 4921 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 241 MET cc_start: 0.1318 (OUTLIER) cc_final: 0.0938 (mtt) REVERT: C 655 MET cc_start: 0.6946 (mmm) cc_final: 0.6483 (mmt) REVERT: C 940 LEU cc_start: 0.3858 (OUTLIER) cc_final: 0.3575 (mp) REVERT: C 995 MET cc_start: 0.3201 (mmm) cc_final: 0.1779 (mtp) REVERT: C 1168 MET cc_start: 0.6952 (mmt) cc_final: 0.6710 (mmm) REVERT: C 1364 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5146 (pp20) REVERT: C 2003 MET cc_start: 0.8379 (mmm) cc_final: 0.7946 (mmp) REVERT: C 2335 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5985 (tmm160) REVERT: C 2756 MET cc_start: 0.1475 (mmt) cc_final: 0.1174 (mmt) REVERT: C 2781 MET cc_start: -0.2253 (ttp) cc_final: -0.3206 (mtt) REVERT: C 2842 MET cc_start: 0.1276 (mpp) cc_final: -0.0120 (mmm) REVERT: C 3818 MET cc_start: 0.3206 (tmm) cc_final: 0.2259 (tmm) REVERT: C 3853 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8249 (t80) REVERT: C 4480 LYS cc_start: 0.5385 (mptt) cc_final: 0.4078 (mmmt) REVERT: I 31 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8068 (mt) REVERT: I 44 ASN cc_start: 0.8060 (m110) cc_final: 0.7834 (t0) REVERT: D 314 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.3862 (pp) REVERT: D 655 MET cc_start: 0.7175 (mmm) cc_final: 0.6499 (mmt) REVERT: D 995 MET cc_start: 0.2609 (mmm) cc_final: 0.1983 (mmm) REVERT: D 1174 MET cc_start: 0.7298 (mtp) cc_final: 0.6915 (mtm) REVERT: D 1364 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6215 (pp20) REVERT: D 2003 MET cc_start: 0.8227 (mmm) cc_final: 0.7651 (mmp) REVERT: D 2247 MET cc_start: 0.7884 (tpp) cc_final: 0.7466 (ttp) REVERT: D 2358 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5018 (mmt180) REVERT: D 2428 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.6019 (tt) REVERT: D 2756 MET cc_start: 0.0709 (mmt) cc_final: 0.0359 (mmt) REVERT: D 2781 MET cc_start: 0.1593 (ttp) cc_final: 0.1213 (ptp) REVERT: D 2843 MET cc_start: 0.0047 (OUTLIER) cc_final: -0.0199 (ttt) REVERT: D 3853 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8233 (t80) REVERT: D 4698 ASN cc_start: 0.4017 (OUTLIER) cc_final: 0.3655 (p0) REVERT: D 4706 MET cc_start: 0.7004 (ttt) cc_final: 0.6770 (ttm) REVERT: J 31 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8093 (mt) REVERT: J 69 LEU cc_start: 0.7608 (tt) cc_final: 0.7404 (tt) outliers start: 331 outliers final: 261 residues processed: 1108 average time/residue: 0.9557 time to fit residues: 1918.0142 Evaluate side-chains 1096 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 807 time to evaluate : 8.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1960 LYS Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 1978 PHE Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2262 GLU Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1680 HIS Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1806 HIS Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1960 LYS Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1978 PHE Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2262 GLU Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2357 SER Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4079 TYR Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4279 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4490 LEU Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1365 THR Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1680 HIS Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2233 MET Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2262 GLU Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2836 LEU Chi-restraints excluded: chain C residue 2902 VAL Chi-restraints excluded: chain C residue 3617 ASN Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3884 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4288 SER Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4509 PHE Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2262 GLU Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2358 ARG Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2481 ASP Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1482 optimal weight: 30.0000 chunk 976 optimal weight: 5.9990 chunk 1572 optimal weight: 5.9990 chunk 959 optimal weight: 40.0000 chunk 746 optimal weight: 1.9990 chunk 1093 optimal weight: 30.0000 chunk 1649 optimal weight: 10.0000 chunk 1518 optimal weight: 40.0000 chunk 1313 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 1014 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3974 GLN ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3613 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3974 GLN ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3974 GLN ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 125860 Z= 0.383 Angle : 0.705 13.732 170648 Z= 0.358 Chirality : 0.042 0.393 19404 Planarity : 0.005 0.081 22256 Dihedral : 4.883 30.289 17657 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.86 % Allowed : 17.40 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.07), residues: 13424 helix: 0.63 (0.06), residues: 6620 sheet: -1.46 (0.14), residues: 1364 loop : -2.21 (0.08), residues: 5440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 557 HIS 0.019 0.002 HIS A1267 PHE 0.027 0.003 PHE A4095 TYR 0.025 0.002 TYR D4724 ARG 0.007 0.001 ARG C4842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 817 time to evaluate : 9.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.2676 (mmm) cc_final: 0.2060 (mmm) REVERT: A 1168 MET cc_start: 0.7129 (mmt) cc_final: 0.6887 (tpp) REVERT: A 1174 MET cc_start: 0.7431 (mtp) cc_final: 0.7052 (mtm) REVERT: A 1215 MET cc_start: 0.6212 (tpp) cc_final: 0.5519 (tpp) REVERT: A 2003 MET cc_start: 0.8338 (mmm) cc_final: 0.7871 (mmp) REVERT: A 2278 MET cc_start: 0.7298 (mmt) cc_final: 0.6918 (tpt) REVERT: A 2358 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.4993 (mmt180) REVERT: A 2459 PHE cc_start: 0.6902 (t80) cc_final: 0.6693 (t80) REVERT: A 2482 PHE cc_start: 0.7606 (t80) cc_final: 0.7345 (t80) REVERT: A 2781 MET cc_start: 0.0874 (ttp) cc_final: -0.0223 (ptt) REVERT: A 2839 MET cc_start: 0.0678 (ttp) cc_final: -0.0931 (mtt) REVERT: A 2843 MET cc_start: 0.0019 (tpp) cc_final: -0.0706 (ttp) REVERT: A 3818 MET cc_start: 0.2567 (tmm) cc_final: 0.2291 (tmm) REVERT: A 3853 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8206 (t80) REVERT: A 4706 MET cc_start: 0.6979 (ttt) cc_final: 0.6727 (ttm) REVERT: G 31 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 236 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4147 (mt) REVERT: B 995 MET cc_start: 0.3185 (mmm) cc_final: 0.1771 (mtp) REVERT: B 1288 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6952 (ptmm) REVERT: B 2003 MET cc_start: 0.8272 (mmm) cc_final: 0.7761 (mmp) REVERT: B 2247 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7615 (ttp) REVERT: B 2358 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5073 (mmt180) REVERT: B 2388 MET cc_start: 0.7904 (mtt) cc_final: 0.7676 (mtt) REVERT: B 2756 MET cc_start: 0.0352 (mmt) cc_final: 0.0083 (mmt) REVERT: B 2781 MET cc_start: 0.2320 (ttp) cc_final: 0.0529 (mtt) REVERT: B 2839 MET cc_start: -0.1376 (ttp) cc_final: -0.2030 (mtt) REVERT: B 2843 MET cc_start: 0.0448 (mmm) cc_final: 0.0155 (ttp) REVERT: B 3818 MET cc_start: 0.3625 (tmm) cc_final: 0.2465 (tmm) REVERT: B 3853 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8272 (t80) REVERT: B 4706 MET cc_start: 0.7047 (ttt) cc_final: 0.6819 (ttm) REVERT: C 241 MET cc_start: 0.1604 (OUTLIER) cc_final: 0.1222 (mtt) REVERT: C 655 MET cc_start: 0.6709 (mmm) cc_final: 0.6473 (mmt) REVERT: C 940 LEU cc_start: 0.3874 (OUTLIER) cc_final: 0.3598 (mp) REVERT: C 995 MET cc_start: 0.2735 (mmm) cc_final: 0.1367 (mtp) REVERT: C 1168 MET cc_start: 0.6924 (mmt) cc_final: 0.6612 (tpp) REVERT: C 1805 LEU cc_start: 0.7042 (tp) cc_final: 0.6766 (tt) REVERT: C 2003 MET cc_start: 0.8397 (mmm) cc_final: 0.7707 (mmp) REVERT: C 2358 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.4530 (mmm160) REVERT: C 2428 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5641 (tp) REVERT: C 2756 MET cc_start: 0.1970 (mmt) cc_final: 0.1500 (mmt) REVERT: C 2781 MET cc_start: -0.1906 (ttp) cc_final: -0.2992 (mtt) REVERT: C 2842 MET cc_start: 0.1417 (mpp) cc_final: -0.0015 (mmm) REVERT: C 3818 MET cc_start: 0.2930 (tmm) cc_final: 0.2285 (tmm) REVERT: C 3853 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8169 (t80) REVERT: C 4706 MET cc_start: 0.7035 (ttt) cc_final: 0.6818 (ttm) REVERT: C 4837 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5582 (tm-30) REVERT: I 31 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8114 (mt) REVERT: D 241 MET cc_start: 0.2300 (OUTLIER) cc_final: 0.2018 (mtp) REVERT: D 314 LEU cc_start: 0.4290 (OUTLIER) cc_final: 0.3544 (pp) REVERT: D 655 MET cc_start: 0.7269 (mmm) cc_final: 0.6677 (mmt) REVERT: D 995 MET cc_start: 0.2576 (mmm) cc_final: 0.1949 (mmm) REVERT: D 1168 MET cc_start: 0.7132 (mmt) cc_final: 0.6880 (tpp) REVERT: D 1174 MET cc_start: 0.7307 (mtp) cc_final: 0.6894 (mtm) REVERT: D 1215 MET cc_start: 0.6167 (tpp) cc_final: 0.5477 (tpp) REVERT: D 2003 MET cc_start: 0.8328 (mmm) cc_final: 0.7786 (mmp) REVERT: D 2247 MET cc_start: 0.7974 (tpp) cc_final: 0.7666 (ttp) REVERT: D 2358 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.5103 (mmt180) REVERT: D 2428 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6056 (tt) REVERT: D 2756 MET cc_start: 0.0576 (mmt) cc_final: 0.0226 (mmt) REVERT: D 2781 MET cc_start: 0.1684 (ttp) cc_final: 0.1193 (ptp) REVERT: D 2843 MET cc_start: -0.0091 (OUTLIER) cc_final: -0.0393 (ttt) REVERT: D 3853 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8143 (t80) REVERT: D 4698 ASN cc_start: 0.3975 (OUTLIER) cc_final: 0.3721 (p0) REVERT: D 4706 MET cc_start: 0.6989 (ttt) cc_final: 0.6748 (ttm) REVERT: J 31 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8093 (mt) outliers start: 337 outliers final: 284 residues processed: 1097 average time/residue: 0.9601 time to fit residues: 1901.2885 Evaluate side-chains 1102 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 795 time to evaluate : 9.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1169 ASN Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1572 PHE Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1895 MET Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 1978 PHE Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2262 GLU Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2350 ILE Chi-restraints excluded: chain A residue 2357 SER Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2401 CYS Chi-restraints excluded: chain A residue 2428 LEU Chi-restraints excluded: chain A residue 2481 ASP Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 3685 PHE Chi-restraints excluded: chain A residue 3800 SER Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3870 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 4041 VAL Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4147 VAL Chi-restraints excluded: chain A residue 4288 SER Chi-restraints excluded: chain A residue 4482 ILE Chi-restraints excluded: chain A residue 4559 VAL Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4617 THR Chi-restraints excluded: chain A residue 4648 VAL Chi-restraints excluded: chain A residue 4652 VAL Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain A residue 4668 LEU Chi-restraints excluded: chain A residue 4698 ASN Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4854 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 713 TRP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1169 ASN Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1288 LYS Chi-restraints excluded: chain B residue 1295 ASN Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1572 PHE Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1806 HIS Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1895 MET Chi-restraints excluded: chain B residue 1960 LYS Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1978 PHE Chi-restraints excluded: chain B residue 2107 ILE Chi-restraints excluded: chain B residue 2247 MET Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2262 GLU Chi-restraints excluded: chain B residue 2292 VAL Chi-restraints excluded: chain B residue 2350 ILE Chi-restraints excluded: chain B residue 2357 SER Chi-restraints excluded: chain B residue 2358 ARG Chi-restraints excluded: chain B residue 2401 CYS Chi-restraints excluded: chain B residue 2481 ASP Chi-restraints excluded: chain B residue 2485 HIS Chi-restraints excluded: chain B residue 3685 PHE Chi-restraints excluded: chain B residue 3800 SER Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3870 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 4041 VAL Chi-restraints excluded: chain B residue 4079 TYR Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4147 VAL Chi-restraints excluded: chain B residue 4279 VAL Chi-restraints excluded: chain B residue 4482 ILE Chi-restraints excluded: chain B residue 4574 LEU Chi-restraints excluded: chain B residue 4617 THR Chi-restraints excluded: chain B residue 4645 ASP Chi-restraints excluded: chain B residue 4648 VAL Chi-restraints excluded: chain B residue 4652 VAL Chi-restraints excluded: chain B residue 4668 LEU Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4854 ILE Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 713 TRP Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 758 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1268 ILE Chi-restraints excluded: chain C residue 1295 ASN Chi-restraints excluded: chain C residue 1340 ASP Chi-restraints excluded: chain C residue 1364 GLU Chi-restraints excluded: chain C residue 1365 THR Chi-restraints excluded: chain C residue 1572 PHE Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1895 MET Chi-restraints excluded: chain C residue 1975 LEU Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2240 ASP Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2262 GLU Chi-restraints excluded: chain C residue 2292 VAL Chi-restraints excluded: chain C residue 2335 ARG Chi-restraints excluded: chain C residue 2350 ILE Chi-restraints excluded: chain C residue 2357 SER Chi-restraints excluded: chain C residue 2358 ARG Chi-restraints excluded: chain C residue 2401 CYS Chi-restraints excluded: chain C residue 2428 LEU Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2481 ASP Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2836 LEU Chi-restraints excluded: chain C residue 2902 VAL Chi-restraints excluded: chain C residue 3617 ASN Chi-restraints excluded: chain C residue 3640 ILE Chi-restraints excluded: chain C residue 3685 PHE Chi-restraints excluded: chain C residue 3800 SER Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 3870 ILE Chi-restraints excluded: chain C residue 3884 ILE Chi-restraints excluded: chain C residue 3885 SER Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 4041 VAL Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4147 VAL Chi-restraints excluded: chain C residue 4279 VAL Chi-restraints excluded: chain C residue 4288 SER Chi-restraints excluded: chain C residue 4482 ILE Chi-restraints excluded: chain C residue 4574 LEU Chi-restraints excluded: chain C residue 4617 THR Chi-restraints excluded: chain C residue 4645 ASP Chi-restraints excluded: chain C residue 4648 VAL Chi-restraints excluded: chain C residue 4652 VAL Chi-restraints excluded: chain C residue 4663 ASP Chi-restraints excluded: chain C residue 4668 LEU Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4837 GLU Chi-restraints excluded: chain C residue 4854 ILE Chi-restraints excluded: chain I residue 26 HIS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 681 HIS Chi-restraints excluded: chain D residue 713 TRP Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1169 ASN Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1295 ASN Chi-restraints excluded: chain D residue 1340 ASP Chi-restraints excluded: chain D residue 1364 GLU Chi-restraints excluded: chain D residue 1572 PHE Chi-restraints excluded: chain D residue 1680 HIS Chi-restraints excluded: chain D residue 1806 HIS Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2262 GLU Chi-restraints excluded: chain D residue 2292 VAL Chi-restraints excluded: chain D residue 2350 ILE Chi-restraints excluded: chain D residue 2358 ARG Chi-restraints excluded: chain D residue 2401 CYS Chi-restraints excluded: chain D residue 2428 LEU Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2843 MET Chi-restraints excluded: chain D residue 3685 PHE Chi-restraints excluded: chain D residue 3800 SER Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 3870 ILE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 4005 SER Chi-restraints excluded: chain D residue 4018 MET Chi-restraints excluded: chain D residue 4041 VAL Chi-restraints excluded: chain D residue 4051 MET Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4147 VAL Chi-restraints excluded: chain D residue 4482 ILE Chi-restraints excluded: chain D residue 4559 VAL Chi-restraints excluded: chain D residue 4574 LEU Chi-restraints excluded: chain D residue 4617 THR Chi-restraints excluded: chain D residue 4645 ASP Chi-restraints excluded: chain D residue 4648 VAL Chi-restraints excluded: chain D residue 4652 VAL Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4698 ASN Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4854 ILE Chi-restraints excluded: chain D residue 4959 LYS Chi-restraints excluded: chain J residue 26 HIS Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 805 optimal weight: 0.9980 chunk 1043 optimal weight: 9.9990 chunk 1399 optimal weight: 5.9990 chunk 402 optimal weight: 2.9990 chunk 1211 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 1315 optimal weight: 6.9990 chunk 550 optimal weight: 2.9990 chunk 1351 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1969 GLN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3974 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117656 restraints weight = 289969.745| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.52 r_work: 0.3547 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 125860 Z= 0.321 Angle : 0.724 59.192 170648 Z= 0.373 Chirality : 0.040 0.310 19404 Planarity : 0.005 0.083 22256 Dihedral : 4.878 30.357 17657 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.81 % Favored : 91.18 % Rotamer: Outliers : 2.90 % Allowed : 17.50 % Favored : 79.60 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.07), residues: 13424 helix: 0.63 (0.06), residues: 6620 sheet: -1.47 (0.14), residues: 1364 loop : -2.22 (0.08), residues: 5440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 557 HIS 0.056 0.002 HIS B1267 PHE 0.025 0.002 PHE A4095 TYR 0.024 0.002 TYR C4724 ARG 0.007 0.001 ARG A1615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30209.55 seconds wall clock time: 527 minutes 24.31 seconds (31644.31 seconds total)