Starting phenix.real_space_refine on Mon Mar 18 00:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxd_11517/03_2024/6zxd_11517.pdb" } resolution = 3.2 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1297 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1645 5.49 5 S 186 5.16 5 C 44539 2.51 5 N 14925 2.21 5 O 19625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 75": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "N TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "x ARG 76": "NH1" <-> "NH2" Residue "x ARG 84": "NH1" <-> "NH2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x ARG 119": "NH1" <-> "NH2" Residue "x GLU 123": "OE1" <-> "OE2" Residue "x ARG 178": "NH1" <-> "NH2" Residue "x ARG 182": "NH1" <-> "NH2" Residue "x ARG 199": "NH1" <-> "NH2" Residue "x ARG 201": "NH1" <-> "NH2" Residue "x ARG 222": "NH1" <-> "NH2" Residue "x ARG 242": "NH1" <-> "NH2" Residue "x ARG 247": "NH1" <-> "NH2" Residue "y ARG 16": "NH1" <-> "NH2" Residue "y ARG 31": "NH1" <-> "NH2" Residue "y GLU 32": "OE1" <-> "OE2" Residue "y ARG 38": "NH1" <-> "NH2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "y ARG 44": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 54": "NH1" <-> "NH2" Residue "y GLU 61": "OE1" <-> "OE2" Residue "y ARG 64": "NH1" <-> "NH2" Residue "y GLU 220": "OE1" <-> "OE2" Residue "y ARG 264": "NH1" <-> "NH2" Residue "F TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "Q PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "T GLU 32": "OE1" <-> "OE2" Residue "T GLU 108": "OE1" <-> "OE2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g GLU 282": "OE1" <-> "OE2" Residue "z ASP 110": "OD1" <-> "OD2" Residue "z GLU 181": "OE1" <-> "OE2" Residue "z ARG 240": "NH1" <-> "NH2" Residue "z GLU 248": "OE1" <-> "OE2" Residue "z GLU 266": "OE1" <-> "OE2" Residue "z ARG 546": "NH1" <-> "NH2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "k ARG 174": "NH1" <-> "NH2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k GLU 216": "OE1" <-> "OE2" Residue "k GLU 229": "OE1" <-> "OE2" Residue "k GLU 243": "OE1" <-> "OE2" Residue "k ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80922 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 35125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1645, 35125 Classifications: {'RNA': 1645} Modifications used: {'rna2p_pur': 128, 'rna2p_pyr': 104, 'rna3p_pur': 744, 'rna3p_pyr': 669} Link IDs: {'rna2p': 232, 'rna3p': 1412} Chain breaks: 13 Chain: "R" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 375 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain breaks: 1 Chain: "x" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2568 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "M" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 588 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 159 Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 346 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 119 Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "z" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1921 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 613 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 292 Chain: "k" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2820 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 36, 'TRANS': 393} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 634 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 234 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" 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 60929 SG CYS y 270 111.943 167.037 150.375 1.00 7.26 S ATOM 60949 SG CYS y 273 115.105 167.323 152.677 1.00 7.07 S ATOM 61046 SG CYS y 285 115.603 168.879 149.322 1.00 6.34 S ATOM 61068 SG CYS y 288 114.810 164.906 149.704 1.00 6.93 S Time building chain proxies: 32.12, per 1000 atoms: 0.40 Number of scatterers: 80922 At special positions: 0 Unit cell: (220.272, 250.983, 204.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 186 16.00 P 1645 15.00 O 19625 8.00 N 14925 7.00 C 44539 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: 28.43 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " Number of angles added : 6 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11052 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 64 sheets defined 34.2% alpha, 15.8% beta 476 base pairs and 903 stacking pairs defined. Time for finding SS restraints: 25.62 Creating SS restraints... Processing helix chain 'R' and resid 6 through 19 removed outlier: 3.649A pdb=" N LYS R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 24 removed outlier: 3.602A pdb=" N ARG R 23 " --> pdb=" O TYR R 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 24 " --> pdb=" O TYR R 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 20 through 24' Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.777A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 59 removed outlier: 3.541A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 81 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.622A pdb=" N GLN A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.622A pdb=" N GLY A 22 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 removed outlier: 4.464A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.883A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.782A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.558A pdb=" N VAL A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.718A pdb=" N LEU A 201 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.981A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.753A pdb=" N THR B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.526A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.169A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.857A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 257 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.503A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 removed outlier: 3.659A pdb=" N VAL C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.134A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.798A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 247 through 262 removed outlier: 4.245A pdb=" N SER E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.536A pdb=" N PHE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.518A pdb=" N GLN G 155 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 229 Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.914A pdb=" N GLU H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 75 through 87 removed outlier: 3.784A pdb=" N GLU H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.933A pdb=" N VAL H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.818A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.549A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 142 through 153 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 204 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 40 through 61 Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.745A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.955A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 171 through 179 removed outlier: 3.714A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 29 Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.537A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 42 Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.975A pdb=" N GLY N 59 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 145 through 150 removed outlier: 3.677A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 3.673A pdb=" N ALA O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.556A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.509A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 75 Processing helix chain 'W' and resid 5 through 19 removed outlier: 3.694A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 43 Processing helix chain 'W' and resid 85 through 93 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 33 through 38 removed outlier: 3.699A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 removed outlier: 3.529A pdb=" N LYS X 135 " --> pdb=" O LEU X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.611A pdb=" N ILE Y 40 " --> pdb=" O PRO Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 80 through 85 Processing helix chain 'Y' and resid 87 through 93 Processing helix chain 'Y' and resid 103 through 115 Processing helix chain 'Y' and resid 121 through 125 removed outlier: 3.624A pdb=" N VAL Y 125 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 removed outlier: 3.698A pdb=" N ARG b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 15 Processing helix chain 'e' and resid 30 through 42 removed outlier: 3.899A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 92 through 101 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 128 through 143 removed outlier: 4.028A pdb=" N LYS x 132 " --> pdb=" O SER x 128 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 150 Processing helix chain 'x' and resid 150 through 155 Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 173 through 185 Processing helix chain 'x' and resid 188 through 199 Processing helix chain 'x' and resid 214 through 230 Processing helix chain 'x' and resid 233 through 246 removed outlier: 3.771A pdb=" N GLY x 239 " --> pdb=" O SER x 235 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 Processing helix chain 'y' and resid 39 through 46 Processing helix chain 'y' and resid 59 through 71 removed outlier: 3.879A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 removed outlier: 3.622A pdb=" N ILE y 84 " --> pdb=" O SER y 80 " (cutoff:3.500A) Processing helix chain 'y' and resid 212 through 217 removed outlier: 4.061A pdb=" N GLN y 216 " --> pdb=" O SER y 212 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 363 through 367 removed outlier: 3.567A pdb=" N TYR y 366 " --> pdb=" O ALA y 363 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE y 367 " --> pdb=" O PRO y 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 363 through 367' Processing helix chain 'd' and resid 15 through 19 removed outlier: 3.727A pdb=" N ARG d 19 " --> pdb=" O GLN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 3.523A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 3.756A pdb=" N GLY D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.535A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.790A pdb=" N GLU D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.718A pdb=" N TYR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 123 " --> pdb=" O CYS D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.718A pdb=" N GLN F 36 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.682A pdb=" N ALA F 58 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS F 59 " --> pdb=" O TYR F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 67 through 76 removed outlier: 3.516A pdb=" N LEU F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 removed outlier: 4.013A pdb=" N ARG F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.521A pdb=" N VAL F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.761A pdb=" N ARG F 159 " --> pdb=" O CYS F 155 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 173 through 183 removed outlier: 4.214A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.562A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 19 removed outlier: 5.301A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 removed outlier: 3.863A pdb=" N SER K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG K 55 " --> pdb=" O SER K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 removed outlier: 4.349A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 18 through 23 removed outlier: 3.554A pdb=" N LEU M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 43 Processing helix chain 'M' and resid 65 through 69 removed outlier: 3.567A pdb=" N LEU M 68 " --> pdb=" O VAL M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 removed outlier: 4.105A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 83 through 88' Processing helix chain 'M' and resid 118 through 122 removed outlier: 3.505A pdb=" N LYS M 121 " --> pdb=" O SER M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 130 Processing helix chain 'P' and resid 21 through 26 removed outlier: 3.781A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.160A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 37 No H-bonds generated for 'chain 'P' and resid 35 through 37' Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 51 through 58 removed outlier: 3.788A pdb=" N LEU P 57 " --> pdb=" O GLN P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 67 removed outlier: 3.746A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA P 67 " --> pdb=" O ALA P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.837A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 119 removed outlier: 3.649A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE P 119 " --> pdb=" O LEU P 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 115 through 119' Processing helix chain 'Q' and resid 38 through 42 removed outlier: 3.624A pdb=" N ILE Q 42 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 47 Processing helix chain 'Q' and resid 48 through 53 Processing helix chain 'Q' and resid 54 through 59 Processing helix chain 'Q' and resid 83 through 99 removed outlier: 4.112A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.635A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 removed outlier: 3.550A pdb=" N LEU Q 120 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 117 through 120' Processing helix chain 'S' and resid 29 through 33 removed outlier: 3.519A pdb=" N ILE S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 60 through 71 removed outlier: 3.501A pdb=" N VAL S 64 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG S 66 " --> pdb=" O ASP S 62 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.674A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 117 removed outlier: 3.847A pdb=" N LEU S 111 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU S 112 " --> pdb=" O ARG S 108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE S 117 " --> pdb=" O ARG S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'T' and resid 10 through 24 removed outlier: 3.760A pdb=" N LYS T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.627A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.793A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 107 removed outlier: 3.578A pdb=" N LEU T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 140 removed outlier: 3.653A pdb=" N ARG T 129 " --> pdb=" O PRO T 125 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP T 130 " --> pdb=" O GLN T 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY T 136 " --> pdb=" O ASP T 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 30 No H-bonds generated for 'chain 'U' and resid 28 through 30' Processing helix chain 'U' and resid 31 through 46 removed outlier: 3.918A pdb=" N VAL U 35 " --> pdb=" O SER U 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY U 42 " --> pdb=" O ASP U 38 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA U 43 " --> pdb=" O LEU U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 101 removed outlier: 3.644A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 61 through 65 Processing helix chain 'Z' and resid 71 through 78 Processing helix chain 'Z' and resid 82 through 88 removed outlier: 3.659A pdb=" N LEU Z 88 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 95 removed outlier: 3.948A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'z' and resid 111 through 117 removed outlier: 3.810A pdb=" N ARG z 114 " --> pdb=" O LYS z 111 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS z 115 " --> pdb=" O VAL z 112 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 162 removed outlier: 3.780A pdb=" N LEU z 162 " --> pdb=" O VAL z 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 158 through 162' Processing helix chain 'z' and resid 163 through 177 removed outlier: 3.637A pdb=" N LYS z 172 " --> pdb=" O MET z 168 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU z 174 " --> pdb=" O LEU z 170 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY z 177 " --> pdb=" O MET z 173 " (cutoff:3.500A) Processing helix chain 'z' and resid 239 through 261 removed outlier: 3.704A pdb=" N VAL z 243 " --> pdb=" O PRO z 239 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS z 244 " --> pdb=" O ARG z 240 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP z 246 " --> pdb=" O MET z 242 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA z 247 " --> pdb=" O VAL z 243 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU z 248 " --> pdb=" O LYS z 244 " (cutoff:3.500A) Processing helix chain 'z' and resid 296 through 316 removed outlier: 4.153A pdb=" N LEU z 305 " --> pdb=" O ARG z 301 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE z 308 " --> pdb=" O TYR z 304 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN z 309 " --> pdb=" O LEU z 305 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR z 310 " --> pdb=" O GLN z 306 " (cutoff:3.500A) Processing helix chain 'z' and resid 352 through 370 removed outlier: 3.901A pdb=" N LEU z 357 " --> pdb=" O ALA z 353 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN z 363 " --> pdb=" O LYS z 359 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN z 365 " --> pdb=" O CYS z 361 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP z 366 " --> pdb=" O ALA z 362 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE z 367 " --> pdb=" O ASN z 363 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE z 368 " --> pdb=" O VAL z 364 " (cutoff:3.500A) Processing helix chain 'z' and resid 377 through 386 removed outlier: 3.773A pdb=" N GLU z 383 " --> pdb=" O ARG z 379 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE z 384 " --> pdb=" O GLU z 380 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL z 385 " --> pdb=" O LEU z 381 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR z 386 " --> pdb=" O PHE z 382 " (cutoff:3.500A) Processing helix chain 'z' and resid 391 through 396 Processing helix chain 'z' and resid 398 through 405 Processing helix chain 'z' and resid 405 through 410 removed outlier: 3.858A pdb=" N ARG z 409 " --> pdb=" O ILE z 405 " (cutoff:3.500A) Processing helix chain 'z' and resid 420 through 426 Processing helix chain 'z' and resid 532 through 545 removed outlier: 3.724A pdb=" N LYS z 536 " --> pdb=" O LYS z 532 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL z 538 " --> pdb=" O ARG z 534 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU z 544 " --> pdb=" O GLU z 540 " (cutoff:3.500A) Processing helix chain 'z' and resid 551 through 559 Processing helix chain 'k' and resid 13 through 19 removed outlier: 3.535A pdb=" N GLU k 19 " --> pdb=" O LEU k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 38 removed outlier: 3.967A pdb=" N ARG k 34 " --> pdb=" O GLY k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 4.337A pdb=" N GLN k 72 " --> pdb=" O PRO k 68 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU k 74 " --> pdb=" O LEU k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 152 Processing helix chain 'k' and resid 195 through 201 removed outlier: 3.939A pdb=" N ALA k 199 " --> pdb=" O PRO k 196 " (cutoff:3.500A) Processing helix chain 'k' and resid 220 through 224 Processing helix chain 'k' and resid 241 through 249 removed outlier: 3.637A pdb=" N SER k 247 " --> pdb=" O GLU k 243 " (cutoff:3.500A) Processing helix chain 'k' and resid 250 through 260 removed outlier: 3.806A pdb=" N VAL k 260 " --> pdb=" O GLU k 256 " (cutoff:3.500A) Processing helix chain 'k' and resid 347 through 362 removed outlier: 3.650A pdb=" N ALA k 351 " --> pdb=" O GLN k 347 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS k 353 " --> pdb=" O GLY k 349 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG k 354 " --> pdb=" O ASN k 350 " (cutoff:3.500A) Processing helix chain 'k' and resid 412 through 420 removed outlier: 4.030A pdb=" N LEU k 418 " --> pdb=" O ARG k 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA k 420 " --> pdb=" O LEU k 416 " (cutoff:3.500A) Processing helix chain 'k' and resid 436 through 441 removed outlier: 3.776A pdb=" N HIS k 440 " --> pdb=" O ARG k 437 " (cutoff:3.500A) Processing helix chain 'k' and resid 492 through 501 removed outlier: 3.920A pdb=" N MET k 496 " --> pdb=" O CYS k 492 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP k 497 " --> pdb=" O LYS k 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 96 through 98 removed outlier: 5.885A pdb=" N ILE R 96 " --> pdb=" O GLN R 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.068A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.734A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.393A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 33 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.393A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 33 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.384A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.059A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 113 removed outlier: 5.447A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AA9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.482A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.879A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.504A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 217 through 220 removed outlier: 6.496A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.793A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR G 48 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB7, first strand: chain 'G' and resid 160 through 161 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 53 removed outlier: 7.607A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 185 through 188 removed outlier: 3.832A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.277A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.418A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 72 through 79 removed outlier: 16.811A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.708A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 92 " --> pdb=" O ARG L 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 52 through 57 removed outlier: 3.551A pdb=" N CYS O 54 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 32 through 39 removed outlier: 5.110A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC7, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.990A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 56 through 58 removed outlier: 6.702A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 56 through 58 removed outlier: 9.851A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.003A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 44 through 47 Processing sheet with id=AD3, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AD4, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.371A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AD6, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AD7, first strand: chain 'y' and resid 111 through 112 removed outlier: 4.142A pdb=" N HIS y 307 " --> pdb=" O THR y 299 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR y 299 " --> pdb=" O HIS y 307 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'd' and resid 53 through 56 removed outlier: 4.414A pdb=" N LEU d 55 " --> pdb=" O ARG U 79 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ARG U 79 " --> pdb=" O LEU d 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 49 through 55 removed outlier: 6.662A pdb=" N VAL U 50 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N HIS U 92 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY U 52 " --> pdb=" O ASP U 90 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP U 90 " --> pdb=" O GLY U 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 34 through 40 removed outlier: 3.944A pdb=" N GLY D 36 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 148 through 153 removed outlier: 4.195A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 123 through 127 removed outlier: 6.465A pdb=" N ASN c 45 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS c 27 " --> pdb=" O ARG c 20 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG c 20 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS c 16 " --> pdb=" O ARG c 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.538A pdb=" N MET K 21 " --> pdb=" O TRP K 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA K 23 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 32 through 33 removed outlier: 3.642A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 52 through 53 removed outlier: 6.511A pdb=" N LEU M 52 " --> pdb=" O VAL M 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'P' and resid 75 through 78 Processing sheet with id=AE9, first strand: chain 'Q' and resid 9 through 15 removed outlier: 3.537A pdb=" N LYS Q 73 " --> pdb=" O THR Q 20 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AF2, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AF3, first strand: chain 'T' and resid 114 through 115 Processing sheet with id=AF4, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.965A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AF6, first strand: chain 'g' and resid 3 through 11 removed outlier: 4.100A pdb=" N GLN g 4 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR g 6 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN g 311 " --> pdb=" O THR g 6 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG g 8 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 21 through 23 Processing sheet with id=AF8, first strand: chain 'g' and resid 40 through 45 removed outlier: 6.037A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 68 through 71 removed outlier: 3.655A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER g 80 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 108 through 112 removed outlier: 3.617A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 151 through 156 removed outlier: 3.673A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER g 167 " --> pdb=" O LYS g 175 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 195 through 200 removed outlier: 6.881A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N CYS g 207 " --> pdb=" O TRP g 219 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP g 219 " --> pdb=" O CYS g 207 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER g 209 " --> pdb=" O MET g 217 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 247 through 251 removed outlier: 6.375A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'z' and resid 120 through 121 removed outlier: 6.513A pdb=" N ASN z 121 " --> pdb=" O GLY z 184 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE z 186 " --> pdb=" O ASN z 121 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS z 196 " --> pdb=" O ASN z 183 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N CYS z 185 " --> pdb=" O VAL z 194 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL z 194 " --> pdb=" O CYS z 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER z 187 " --> pdb=" O ALA z 192 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA z 192 " --> pdb=" O SER z 187 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE z 207 " --> pdb=" O TYR z 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA z 197 " --> pdb=" O ARG z 205 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET z 269 " --> pdb=" O VAL z 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'z' and resid 320 through 321 Processing sheet with id=AG7, first strand: chain 'z' and resid 330 through 333 Processing sheet with id=AG8, first strand: chain 'k' and resid 23 through 26 removed outlier: 3.648A pdb=" N ARG k 83 " --> pdb=" O VAL k 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU k 80 " --> pdb=" O VAL k 103 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU k 158 " --> pdb=" O ALA k 185 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU k 184 " --> pdb=" O ASP k 208 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'k' and resid 337 through 340 removed outlier: 3.796A pdb=" N VAL k 483 " --> pdb=" O VAL k 337 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU k 482 " --> pdb=" O ALA k 376 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA k 376 " --> pdb=" O GLU k 482 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'k' and resid 391 through 392 removed outlier: 3.550A pdb=" N TYR k 448 " --> pdb=" O ARG k 392 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1181 hydrogen bonds 1840 hydrogen bond angles 0 basepair planarities 476 basepair parallelities 903 stacking parallelities Total time for adding SS restraints: 59.33 Time building geometry restraints manager: 31.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12962 1.33 - 1.45: 29848 1.45 - 1.57: 39425 1.57 - 1.69: 3273 1.69 - 1.82: 289 Bond restraints: 85797 Sorted by residual: bond pdb=" O3' C 21254 " pdb=" P G 21255 " ideal model delta sigma weight residual 1.607 1.530 0.077 1.50e-02 4.44e+03 2.63e+01 bond pdb=" O3' G 21255 " pdb=" P G 21256 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' G 21257 " pdb=" P A 21258 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.53e+00 bond pdb=" P C 21254 " pdb=" OP2 C 21254 " ideal model delta sigma weight residual 1.485 1.436 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" O3' U 21667 " pdb=" P U 21668 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.39e+00 ... (remaining 85792 not shown) Histogram of bond angle deviations from ideal: 96.77 - 105.05: 8177 105.05 - 113.33: 51049 113.33 - 121.61: 43764 121.61 - 129.89: 19731 129.89 - 138.17: 1077 Bond angle restraints: 123798 Sorted by residual: angle pdb=" N LEU k 242 " pdb=" CA LEU k 242 " pdb=" C LEU k 242 " ideal model delta sigma weight residual 112.23 102.87 9.36 1.26e+00 6.30e-01 5.52e+01 angle pdb=" N VAL x 207 " pdb=" CA VAL x 207 " pdb=" C VAL x 207 " ideal model delta sigma weight residual 113.53 107.47 6.06 9.80e-01 1.04e+00 3.82e+01 angle pdb=" N GLN d 4 " pdb=" CA GLN d 4 " pdb=" C GLN d 4 " ideal model delta sigma weight residual 112.38 119.05 -6.67 1.22e+00 6.72e-01 2.99e+01 angle pdb=" C4' C 21247 " pdb=" C3' C 21247 " pdb=" O3' C 21247 " ideal model delta sigma weight residual 109.40 101.29 8.11 1.50e+00 4.44e-01 2.93e+01 angle pdb=" C3' C 21403 " pdb=" O3' C 21403 " pdb=" P U 21404 " ideal model delta sigma weight residual 120.20 127.96 -7.76 1.50e+00 4.44e-01 2.68e+01 ... (remaining 123793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 49615 35.78 - 71.57: 4238 71.57 - 107.35: 520 107.35 - 143.13: 25 143.13 - 178.91: 31 Dihedral angle restraints: 54429 sinusoidal: 37345 harmonic: 17084 Sorted by residual: dihedral pdb=" CA ALA F 40 " pdb=" C ALA F 40 " pdb=" N VAL F 41 " pdb=" CA VAL F 41 " ideal model delta harmonic sigma weight residual -180.00 -130.63 -49.37 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA PRO D 194 " pdb=" C PRO D 194 " pdb=" N THR D 195 " pdb=" CA THR D 195 " ideal model delta harmonic sigma weight residual -180.00 -133.14 -46.86 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" O4' C 21618 " pdb=" C1' C 21618 " pdb=" N1 C 21618 " pdb=" C2 C 21618 " ideal model delta sinusoidal sigma weight residual -160.00 18.11 -178.11 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 54426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 13497 0.080 - 0.161: 1626 0.161 - 0.241: 134 0.241 - 0.321: 37 0.321 - 0.402: 9 Chirality restraints: 15303 Sorted by residual: chirality pdb=" C3' U 21232 " pdb=" C4' U 21232 " pdb=" O3' U 21232 " pdb=" C2' U 21232 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' A 2 980 " pdb=" C4' A 2 980 " pdb=" O3' A 2 980 " pdb=" C2' A 2 980 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 15300 not shown) Planarity restraints: 9680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 495 " 0.056 2.00e-02 2.50e+03 2.73e-02 1.68e+01 pdb=" N1 U 2 495 " -0.053 2.00e-02 2.50e+03 pdb=" C2 U 2 495 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U 2 495 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U 2 495 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U 2 495 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U 2 495 " 0.019 2.00e-02 2.50e+03 pdb=" C5 U 2 495 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U 2 495 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 236 " -0.032 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE C 236 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE C 236 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 236 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 236 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 236 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21658 " 0.045 2.00e-02 2.50e+03 1.85e-02 1.03e+01 pdb=" N9 G 21658 " -0.039 2.00e-02 2.50e+03 pdb=" C8 G 21658 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G 21658 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 21658 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 21658 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G 21658 " 0.018 2.00e-02 2.50e+03 pdb=" N1 G 21658 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 21658 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 21658 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 21658 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G 21658 " -0.010 2.00e-02 2.50e+03 ... (remaining 9677 not shown) Histogram of nonbonded interaction distances: 0.25 - 1.18: 1 1.18 - 2.11: 16 2.11 - 3.04: 42959 3.04 - 3.97: 229224 3.97 - 4.90: 419544 Warning: very small nonbonded interaction distances. Nonbonded interactions: 691744 Sorted by model distance: nonbonded pdb=" OP1 G 21540 " pdb=" NZ LYS T 43 " model vdw 0.254 2.520 nonbonded pdb=" P G 21540 " pdb=" NZ LYS T 43 " model vdw 1.322 3.480 nonbonded pdb=" N7 A 21284 " pdb=" N6 A 21313 " model vdw 1.417 2.600 nonbonded pdb=" N1 A 21287 " pdb=" C8 A 21313 " model vdw 1.491 3.340 nonbonded pdb=" OP1 G 21540 " pdb=" CE LYS T 43 " model vdw 1.590 3.440 ... (remaining 691739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.090 Extract box with map and model: 12.200 Check model and map are aligned: 0.880 Set scattering table: 0.560 Process input model: 221.620 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.007 0.089 85797 Z= 0.451 Angle : 0.939 17.457 123798 Z= 0.488 Chirality : 0.055 0.402 15303 Planarity : 0.006 0.065 9680 Dihedral : 22.102 178.913 43377 Min Nonbonded Distance : 0.254 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.59 % Rotamer: Outliers : 0.21 % Allowed : 7.64 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.09 % 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: -3.93 (0.09), residues: 5844 helix: -2.85 (0.09), residues: 1770 sheet: -2.13 (0.15), residues: 995 loop : -2.63 (0.09), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP g 247 HIS 0.020 0.002 HIS P 79 PHE 0.066 0.003 PHE C 236 TYR 0.024 0.003 TYR Z 65 ARG 0.015 0.001 ARG Q 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1121 time to evaluate : 5.660 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 ILE cc_start: 0.7997 (mm) cc_final: 0.7787 (mm) REVERT: J 13 TYR cc_start: 0.8247 (p90) cc_final: 0.7872 (p90) REVERT: O 147 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7871 (mtm180) REVERT: b 36 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7464 (mttm) REVERT: D 123 LEU cc_start: 0.7540 (tp) cc_final: 0.7283 (tp) REVERT: D 189 MET cc_start: 0.7800 (ttt) cc_final: 0.7554 (ttt) REVERT: k 226 LYS cc_start: 0.7108 (mttm) cc_final: 0.6634 (mmtm) outliers start: 10 outliers final: 5 residues processed: 1130 average time/residue: 0.8876 time to fit residues: 1612.1395 Evaluate side-chains 845 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 840 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 628 optimal weight: 20.0000 chunk 563 optimal weight: 50.0000 chunk 312 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 583 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 354 optimal weight: 0.9990 chunk 434 optimal weight: 1.9990 chunk 675 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN R 83 ASN R 116 ASN A 84 GLN A 131 HIS A 165 ASN B 40 ASN B 53 GLN B 95 ASN C 172 ASN E 8 HIS E 98 ASN E 232 ASN G 56 ASN H 91 HIS ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN H 193 GLN I 88 ASN I 116 HIS I 165 GLN J 125 HIS L 18 GLN L 83 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 HIS N 58 HIS O 26 ASN O 113 GLN X 46 HIS X 63 ASN X 110 HIS Y 89 HIS b 65 GLN e 22 GLN x 232 ASN y 26 ASN y 102 HIS y 348 GLN y 360 ASN y 386 GLN D 101 GLN F 83 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN F 114 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN P 103 ASN Q 11 GLN S 42 HIS S 72 GLN T 51 ASN T 105 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 HIS Z 112 ASN g 64 HIS g 215 GLN g 226 HIS g 237 ASN z 121 ASN z 183 ASN ** z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 GLN k 78 HIS k 139 ASN k 156 GLN k 189 ASN k 211 ASN k 212 ASN k 235 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 85797 Z= 0.230 Angle : 0.648 13.353 123798 Z= 0.332 Chirality : 0.041 0.306 15303 Planarity : 0.005 0.071 9680 Dihedral : 23.228 179.161 32199 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.15 % Allowed : 12.97 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.78 (0.10), residues: 5844 helix: -1.36 (0.11), residues: 1800 sheet: -1.76 (0.15), residues: 1011 loop : -2.17 (0.10), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 45 HIS 0.007 0.001 HIS F 101 PHE 0.035 0.002 PHE C 236 TYR 0.046 0.001 TYR G 28 ARG 0.008 0.000 ARG y 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 921 time to evaluate : 4.823 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: E 136 ILE cc_start: 0.8100 (mm) cc_final: 0.7812 (mm) REVERT: J 13 TYR cc_start: 0.8298 (p90) cc_final: 0.7907 (p90) REVERT: J 132 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: N 110 ASP cc_start: 0.7701 (t70) cc_final: 0.7423 (t0) REVERT: O 65 ASP cc_start: 0.7832 (m-30) cc_final: 0.7618 (m-30) REVERT: O 147 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8065 (mtm110) REVERT: W 18 GLU cc_start: 0.7861 (tp30) cc_final: 0.7387 (mm-30) REVERT: W 49 GLU cc_start: 0.7426 (pt0) cc_final: 0.7211 (pt0) REVERT: X 24 ASP cc_start: 0.7255 (t0) cc_final: 0.6935 (t70) REVERT: b 36 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7596 (mttm) REVERT: Q 140 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.7385 (mmt-90) REVERT: Q 143 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8394 (ttmt) REVERT: z 250 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6631 (tm-30) REVERT: k 226 LYS cc_start: 0.6992 (mttm) cc_final: 0.6490 (mmtm) outliers start: 101 outliers final: 66 residues processed: 974 average time/residue: 0.8322 time to fit residues: 1352.4209 Evaluate side-chains 893 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 824 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 93 LEU Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 298 LEU Chi-restraints excluded: chain z residue 183 ASN Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain k residue 103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 375 optimal weight: 7.9990 chunk 209 optimal weight: 0.0670 chunk 562 optimal weight: 0.1980 chunk 460 optimal weight: 0.9980 chunk 186 optimal weight: 0.0770 chunk 676 optimal weight: 0.0470 chunk 731 optimal weight: 7.9990 chunk 602 optimal weight: 0.5980 chunk 671 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 542 optimal weight: 0.8980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN R 83 ASN B 40 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS E 214 ASN E 232 ASN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 HIS H 165 ASN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN y 271 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS S 72 GLN T 51 ASN T 91 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS ** z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 HIS k 76 GLN ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 212 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 85797 Z= 0.133 Angle : 0.561 15.201 123798 Z= 0.288 Chirality : 0.037 0.328 15303 Planarity : 0.004 0.055 9680 Dihedral : 23.043 179.500 32199 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 1.86 % Allowed : 15.02 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.02 (0.10), residues: 5844 helix: -0.53 (0.12), residues: 1824 sheet: -1.34 (0.16), residues: 992 loop : -1.85 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 30 HIS 0.005 0.001 HIS F 101 PHE 0.023 0.001 PHE x 96 TYR 0.034 0.001 TYR G 28 ARG 0.012 0.000 ARG c 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 930 time to evaluate : 4.884 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 172 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7258 (m110) REVERT: C 174 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 267 GLN cc_start: 0.7927 (tt0) cc_final: 0.7680 (tt0) REVERT: E 108 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7504 (mtm180) REVERT: E 136 ILE cc_start: 0.7805 (mm) cc_final: 0.7516 (mm) REVERT: G 132 ARG cc_start: 0.7202 (ptm160) cc_final: 0.6827 (ptp-170) REVERT: J 13 TYR cc_start: 0.8276 (p90) cc_final: 0.7842 (p90) REVERT: J 143 ASN cc_start: 0.7779 (t0) cc_final: 0.7511 (t0) REVERT: O 147 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7975 (mtm110) REVERT: W 18 GLU cc_start: 0.7664 (tp30) cc_final: 0.7439 (mm-30) REVERT: W 49 GLU cc_start: 0.7158 (pt0) cc_final: 0.6957 (pt0) REVERT: b 36 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7734 (mttm) REVERT: x 135 ASP cc_start: 0.6864 (m-30) cc_final: 0.6633 (m-30) REVERT: Q 140 ARG cc_start: 0.8351 (mmt-90) cc_final: 0.7256 (mmt-90) REVERT: T 75 MET cc_start: 0.8067 (tpp) cc_final: 0.7739 (mmt) REVERT: U 83 ARG cc_start: 0.8403 (mtt90) cc_final: 0.8118 (mtt-85) REVERT: k 226 LYS cc_start: 0.6905 (mttm) cc_final: 0.6397 (mmtm) outliers start: 87 outliers final: 54 residues processed: 975 average time/residue: 0.7969 time to fit residues: 1299.7902 Evaluate side-chains 877 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 820 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 298 LEU Chi-restraints excluded: chain z residue 254 LEU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 668 optimal weight: 0.0670 chunk 508 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 454 optimal weight: 2.9990 chunk 679 optimal weight: 7.9990 chunk 719 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 643 optimal weight: 0.0980 chunk 193 optimal weight: 0.7980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN A 215 GLN E 179 ASN G 59 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN L 112 HIS V 47 ASN X 63 ASN ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS T 63 HIS T 137 GLN U 81 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 ASN z 183 ASN z 196 HIS z 273 HIS ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 212 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 85797 Z= 0.147 Angle : 0.549 15.995 123798 Z= 0.280 Chirality : 0.037 0.318 15303 Planarity : 0.004 0.059 9680 Dihedral : 22.910 179.641 32198 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 2.41 % Allowed : 16.30 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.58 (0.11), residues: 5844 helix: -0.06 (0.12), residues: 1836 sheet: -1.12 (0.16), residues: 971 loop : -1.65 (0.11), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 259 HIS 0.017 0.001 HIS g 64 PHE 0.021 0.001 PHE e 42 TYR 0.024 0.001 TYR G 28 ARG 0.007 0.000 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 847 time to evaluate : 4.830 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: symmetry clash revert: symmetry clash REVERT: E 108 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: E 136 ILE cc_start: 0.7882 (mm) cc_final: 0.7544 (mm) REVERT: G 132 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6882 (ptp-170) REVERT: J 13 TYR cc_start: 0.8303 (p90) cc_final: 0.7897 (p90) REVERT: J 132 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: J 143 ASN cc_start: 0.7797 (t0) cc_final: 0.7488 (t0) REVERT: N 110 ASP cc_start: 0.7494 (t70) cc_final: 0.7238 (t0) REVERT: O 147 ARG cc_start: 0.8243 (mmm160) cc_final: 0.8019 (mtm110) REVERT: W 49 GLU cc_start: 0.7192 (pt0) cc_final: 0.6991 (pt0) REVERT: X 24 ASP cc_start: 0.7176 (t0) cc_final: 0.6975 (t70) REVERT: b 36 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7804 (mttm) REVERT: x 135 ASP cc_start: 0.6980 (m-30) cc_final: 0.6727 (m-30) REVERT: Q 140 ARG cc_start: 0.8397 (mmt-90) cc_final: 0.7380 (mmt-90) REVERT: k 226 LYS cc_start: 0.6919 (mttm) cc_final: 0.6411 (mmtm) outliers start: 113 outliers final: 83 residues processed: 900 average time/residue: 0.7919 time to fit residues: 1202.1763 Evaluate side-chains 889 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 804 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 298 LEU Chi-restraints excluded: chain z residue 183 ASN Chi-restraints excluded: chain z residue 204 SER Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 598 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 535 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 613 optimal weight: 5.9990 chunk 497 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 367 optimal weight: 0.0470 chunk 645 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN R 116 ASN C 267 GLN G 13 GLN G 59 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN V 47 ASN W 44 HIS X 63 ASN b 19 HIS e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS F 83 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS z 273 HIS ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 85797 Z= 0.360 Angle : 0.683 15.242 123798 Z= 0.344 Chirality : 0.044 0.327 15303 Planarity : 0.005 0.060 9680 Dihedral : 23.001 178.919 32196 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 3.37 % Allowed : 17.43 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.55 (0.11), residues: 5844 helix: -0.05 (0.12), residues: 1835 sheet: -1.10 (0.16), residues: 972 loop : -1.61 (0.11), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 64 HIS 0.010 0.001 HIS S 135 PHE 0.030 0.002 PHE C 236 TYR 0.021 0.002 TYR K 78 ARG 0.016 0.001 ARG g 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 814 time to evaluate : 4.852 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: symmetry clash revert: symmetry clash REVERT: B 177 GLN cc_start: 0.7722 (pt0) cc_final: 0.7455 (pt0) REVERT: E 136 ILE cc_start: 0.8132 (mm) cc_final: 0.7833 (mm) REVERT: G 132 ARG cc_start: 0.7382 (ptm160) cc_final: 0.6938 (ptp-170) REVERT: I 124 LYS cc_start: 0.6968 (mmtt) cc_final: 0.6747 (mmtt) REVERT: J 13 TYR cc_start: 0.8413 (p90) cc_final: 0.8103 (p90) REVERT: J 132 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: N 110 ASP cc_start: 0.7780 (t70) cc_final: 0.7501 (t0) REVERT: V 62 MET cc_start: 0.7369 (ptm) cc_final: 0.6868 (ppp) REVERT: W 49 GLU cc_start: 0.7409 (pt0) cc_final: 0.7184 (pt0) REVERT: Y 19 GLN cc_start: 0.8225 (mp10) cc_final: 0.8017 (mp10) REVERT: b 36 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7842 (mttm) REVERT: x 135 ASP cc_start: 0.7059 (m-30) cc_final: 0.6787 (m-30) REVERT: y 248 MET cc_start: 0.3679 (OUTLIER) cc_final: 0.3476 (ttp) REVERT: g 36 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5230 (ttt90) REVERT: z 178 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7582 (mp) REVERT: k 226 LYS cc_start: 0.6837 (mttm) cc_final: 0.6411 (mmtm) outliers start: 158 outliers final: 123 residues processed: 897 average time/residue: 0.7983 time to fit residues: 1202.0377 Evaluate side-chains 923 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 796 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 248 MET Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 308 MET Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 36 ARG Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 187 SER Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 210 SER Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 241 optimal weight: 3.9990 chunk 647 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 422 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 719 optimal weight: 1.9990 chunk 597 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 377 optimal weight: 0.0020 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN B 40 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN H 91 HIS H 114 GLN H 165 ASN I 88 ASN L 141 ASN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN F 114 ASN F 179 ASN S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS z 183 ASN z 273 HIS ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 85797 Z= 0.177 Angle : 0.573 16.237 123798 Z= 0.292 Chirality : 0.038 0.309 15303 Planarity : 0.004 0.055 9680 Dihedral : 22.943 178.097 32196 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.05 % Allowed : 18.62 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.25 (0.11), residues: 5844 helix: 0.29 (0.12), residues: 1828 sheet: -1.02 (0.16), residues: 977 loop : -1.46 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 45 HIS 0.030 0.001 HIS g 64 PHE 0.024 0.001 PHE e 42 TYR 0.018 0.001 TYR Q 99 ARG 0.006 0.000 ARG U 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 826 time to evaluate : 5.580 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: symmetry clash REVERT: R 44 LYS cc_start: 0.7969 (mttp) cc_final: 0.7763 (mttt) REVERT: B 177 GLN cc_start: 0.7700 (pt0) cc_final: 0.7441 (pt0) REVERT: E 136 ILE cc_start: 0.7965 (mm) cc_final: 0.7674 (mm) REVERT: G 65 GLN cc_start: 0.7797 (tp40) cc_final: 0.7473 (tp40) REVERT: I 124 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6694 (mmtt) REVERT: J 13 TYR cc_start: 0.8418 (p90) cc_final: 0.8129 (p90) REVERT: J 132 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: N 110 ASP cc_start: 0.7594 (t70) cc_final: 0.7347 (t0) REVERT: W 49 GLU cc_start: 0.7335 (pt0) cc_final: 0.7105 (pt0) REVERT: W 115 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: X 24 ASP cc_start: 0.7224 (t0) cc_final: 0.6945 (t70) REVERT: b 36 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7814 (mttm) REVERT: x 135 ASP cc_start: 0.7055 (m-30) cc_final: 0.6783 (m-30) REVERT: d 5 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.6069 (mt0) REVERT: U 86 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7488 (ttmt) REVERT: z 105 MET cc_start: 0.2328 (pmm) cc_final: 0.2104 (pmm) REVERT: z 172 LYS cc_start: 0.7194 (mtmt) cc_final: 0.6762 (mttt) REVERT: z 178 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7477 (mp) REVERT: z 250 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6877 (tm-30) REVERT: k 226 LYS cc_start: 0.6799 (mttm) cc_final: 0.6395 (mmtm) outliers start: 143 outliers final: 115 residues processed: 905 average time/residue: 0.8004 time to fit residues: 1214.8639 Evaluate side-chains 917 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 798 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 5 GLN Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain z residue 118 ASN Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 183 ASN Chi-restraints excluded: chain z residue 187 SER Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 204 SER Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 277 MET Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 694 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 410 optimal weight: 7.9990 chunk 525 optimal weight: 6.9990 chunk 407 optimal weight: 3.9990 chunk 605 optimal weight: 0.6980 chunk 401 optimal weight: 2.9990 chunk 717 optimal weight: 10.0000 chunk 448 optimal weight: 3.9990 chunk 437 optimal weight: 8.9990 chunk 331 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN G 59 GLN H 165 ASN I 7 ASN I 88 ASN I 146 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN S 42 HIS S 72 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS z 183 ASN z 273 HIS ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 85797 Z= 0.193 Angle : 0.576 16.244 123798 Z= 0.293 Chirality : 0.038 0.303 15303 Planarity : 0.004 0.058 9680 Dihedral : 22.900 178.216 32196 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 3.22 % Allowed : 19.03 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.11), residues: 5844 helix: 0.44 (0.12), residues: 1834 sheet: -1.00 (0.16), residues: 990 loop : -1.40 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 45 HIS 0.007 0.001 HIS F 101 PHE 0.021 0.001 PHE e 42 TYR 0.019 0.001 TYR K 57 ARG 0.008 0.000 ARG y 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 811 time to evaluate : 5.559 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 267 GLN cc_start: 0.7883 (tt0) cc_final: 0.7590 (tt0) REVERT: E 136 ILE cc_start: 0.7963 (mm) cc_final: 0.7669 (mm) REVERT: G 65 GLN cc_start: 0.7747 (tp40) cc_final: 0.7450 (tp40) REVERT: I 7 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6838 (m110) REVERT: J 13 TYR cc_start: 0.8430 (p90) cc_final: 0.8136 (p90) REVERT: J 132 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: N 110 ASP cc_start: 0.7600 (t70) cc_final: 0.7359 (t0) REVERT: W 49 GLU cc_start: 0.7335 (pt0) cc_final: 0.7102 (pt0) REVERT: X 24 ASP cc_start: 0.7229 (t0) cc_final: 0.6954 (t70) REVERT: b 36 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7839 (mttm) REVERT: x 135 ASP cc_start: 0.7061 (m-30) cc_final: 0.6779 (m-30) REVERT: y 330 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7312 (mmtm) REVERT: d 32 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7978 (ptm-80) REVERT: z 105 MET cc_start: 0.2602 (pmm) cc_final: 0.2251 (pmm) REVERT: z 172 LYS cc_start: 0.7185 (mtmt) cc_final: 0.6846 (mttt) REVERT: z 178 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7557 (mp) REVERT: k 226 LYS cc_start: 0.6796 (mttm) cc_final: 0.6394 (mmtm) outliers start: 151 outliers final: 124 residues processed: 898 average time/residue: 0.8062 time to fit residues: 1212.9006 Evaluate side-chains 930 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 801 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 22 ASP Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 308 MET Chi-restraints excluded: chain y residue 330 LYS Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain z residue 118 ASN Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 187 SER Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 277 MET Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 443 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 428 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 488 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 563 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN I 88 ASN X 63 ASN e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 183 ASN z 273 HIS k 76 GLN ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 85797 Z= 0.199 Angle : 0.579 16.378 123798 Z= 0.294 Chirality : 0.038 0.300 15303 Planarity : 0.004 0.061 9680 Dihedral : 22.876 178.501 32196 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 3.18 % Allowed : 19.60 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.11), residues: 5844 helix: 0.52 (0.12), residues: 1836 sheet: -0.99 (0.16), residues: 1009 loop : -1.34 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 8 HIS 0.007 0.001 HIS F 101 PHE 0.019 0.001 PHE x 96 TYR 0.017 0.001 TYR I 113 ARG 0.007 0.000 ARG x 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 817 time to evaluate : 4.929 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 ILE cc_start: 0.7963 (mm) cc_final: 0.7662 (mm) REVERT: G 32 MET cc_start: 0.7660 (mtp) cc_final: 0.7438 (mtp) REVERT: G 65 GLN cc_start: 0.7727 (tp40) cc_final: 0.7419 (tp40) REVERT: G 91 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: J 13 TYR cc_start: 0.8434 (p90) cc_final: 0.8194 (p90) REVERT: J 132 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: N 110 ASP cc_start: 0.7608 (t70) cc_final: 0.7361 (t0) REVERT: V 64 GLU cc_start: 0.6820 (mp0) cc_final: 0.6365 (mp0) REVERT: W 49 GLU cc_start: 0.7324 (pt0) cc_final: 0.7068 (pt0) REVERT: W 115 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: X 24 ASP cc_start: 0.7233 (t0) cc_final: 0.6958 (t70) REVERT: Y 19 GLN cc_start: 0.8190 (mp10) cc_final: 0.7984 (mp10) REVERT: b 36 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7829 (mttm) REVERT: x 135 ASP cc_start: 0.7080 (m-30) cc_final: 0.6786 (m-30) REVERT: y 330 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7240 (mmtm) REVERT: d 32 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7972 (ptm-80) REVERT: Q 114 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5841 (mm-40) REVERT: U 83 ARG cc_start: 0.8414 (mtt90) cc_final: 0.8189 (mtt-85) REVERT: z 105 MET cc_start: 0.2784 (pmm) cc_final: 0.2361 (pmm) REVERT: z 172 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6926 (mttt) REVERT: z 178 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7629 (mp) REVERT: k 226 LYS cc_start: 0.6783 (mttm) cc_final: 0.6391 (mmtm) REVERT: k 237 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7986 (mm) outliers start: 149 outliers final: 132 residues processed: 897 average time/residue: 0.7959 time to fit residues: 1199.2261 Evaluate side-chains 944 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 804 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 22 ASP Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 308 MET Chi-restraints excluded: chain y residue 330 LYS Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 114 GLN Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain z residue 118 ASN Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 183 ASN Chi-restraints excluded: chain z residue 187 SER Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 204 SER Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 277 MET Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 151 CYS Chi-restraints excluded: chain k residue 210 SER Chi-restraints excluded: chain k residue 237 LEU Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 652 optimal weight: 20.0000 chunk 686 optimal weight: 30.0000 chunk 626 optimal weight: 3.9990 chunk 668 optimal weight: 7.9990 chunk 402 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 524 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 603 optimal weight: 9.9990 chunk 632 optimal weight: 20.0000 chunk 665 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN H 165 ASN I 7 ASN I 146 GLN N 49 GLN X 63 ASN e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 17 HIS ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 183 ASN z 273 HIS k 76 GLN ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 85797 Z= 0.314 Angle : 0.655 15.560 123798 Z= 0.331 Chirality : 0.042 0.322 15303 Planarity : 0.005 0.064 9680 Dihedral : 22.917 179.367 32196 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 3.35 % Allowed : 19.73 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.11), residues: 5844 helix: 0.40 (0.12), residues: 1847 sheet: -0.96 (0.16), residues: 996 loop : -1.38 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 64 HIS 0.008 0.001 HIS J 156 PHE 0.021 0.002 PHE J 147 TYR 0.018 0.002 TYR I 113 ARG 0.007 0.001 ARG O 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 808 time to evaluate : 5.029 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 GLN cc_start: 0.7906 (pt0) cc_final: 0.7667 (pt0) REVERT: C 267 GLN cc_start: 0.7978 (tt0) cc_final: 0.7603 (tt0) REVERT: E 136 ILE cc_start: 0.8066 (mm) cc_final: 0.7759 (mm) REVERT: G 91 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: I 7 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6864 (m110) REVERT: J 132 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: J 169 ARG cc_start: 0.7564 (tpt170) cc_final: 0.7259 (tpt170) REVERT: N 110 ASP cc_start: 0.7818 (t70) cc_final: 0.7531 (t0) REVERT: V 64 GLU cc_start: 0.6910 (mp0) cc_final: 0.6528 (mp0) REVERT: W 49 GLU cc_start: 0.7468 (pt0) cc_final: 0.7193 (pt0) REVERT: W 115 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: b 36 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7840 (mttm) REVERT: x 135 ASP cc_start: 0.7105 (m-30) cc_final: 0.6810 (m-30) REVERT: y 330 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7288 (mmtm) REVERT: d 5 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5901 (mt0) REVERT: d 32 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7944 (ptm-80) REVERT: z 178 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7809 (mp) REVERT: k 226 LYS cc_start: 0.6793 (mttm) cc_final: 0.6385 (mmtm) REVERT: k 237 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8019 (mm) REVERT: k 244 LYS cc_start: 0.7126 (mttt) cc_final: 0.6813 (mtpt) outliers start: 157 outliers final: 137 residues processed: 902 average time/residue: 0.8067 time to fit residues: 1215.5782 Evaluate side-chains 941 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 795 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain b residue 17 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 22 ASP Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain y residue 308 MET Chi-restraints excluded: chain y residue 330 LYS Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 5 GLN Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 114 GLN Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain z residue 118 ASN Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 183 ASN Chi-restraints excluded: chain z residue 187 SER Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 277 MET Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 151 CYS Chi-restraints excluded: chain k residue 210 SER Chi-restraints excluded: chain k residue 237 LEU Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 438 optimal weight: 0.6980 chunk 706 optimal weight: 6.9990 chunk 431 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 491 optimal weight: 2.9990 chunk 741 optimal weight: 30.0000 chunk 682 optimal weight: 3.9990 chunk 590 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 455 optimal weight: 0.7980 chunk 361 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS H 165 ASN X 63 ASN ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 273 HIS k 76 GLN ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 85797 Z= 0.199 Angle : 0.597 15.790 123798 Z= 0.304 Chirality : 0.039 0.291 15303 Planarity : 0.004 0.099 9680 Dihedral : 22.917 178.900 32196 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 2.88 % Allowed : 20.39 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.11), residues: 5844 helix: 0.50 (0.12), residues: 1848 sheet: -0.94 (0.16), residues: 1000 loop : -1.32 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 82 HIS 0.017 0.001 HIS I 9 PHE 0.019 0.001 PHE x 96 TYR 0.019 0.001 TYR R 20 ARG 0.007 0.000 ARG I 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11688 Ramachandran restraints generated. 5844 Oldfield, 0 Emsley, 5844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 810 time to evaluate : 4.995 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 GLN cc_start: 0.7860 (pt0) cc_final: 0.7634 (pt0) REVERT: C 267 GLN cc_start: 0.7919 (tt0) cc_final: 0.7588 (tt0) REVERT: E 87 MET cc_start: 0.7941 (mmt) cc_final: 0.7672 (mmt) REVERT: E 136 ILE cc_start: 0.7991 (mm) cc_final: 0.7693 (mm) REVERT: G 65 GLN cc_start: 0.7813 (tp40) cc_final: 0.7442 (tp40) REVERT: G 91 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: J 132 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: J 169 ARG cc_start: 0.7486 (tpt170) cc_final: 0.7146 (tpt170) REVERT: N 110 ASP cc_start: 0.7694 (t70) cc_final: 0.7427 (t0) REVERT: V 64 GLU cc_start: 0.6771 (mp0) cc_final: 0.6410 (mp0) REVERT: W 49 GLU cc_start: 0.7385 (pt0) cc_final: 0.7123 (pt0) REVERT: X 24 ASP cc_start: 0.7232 (t0) cc_final: 0.6957 (t70) REVERT: b 36 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7849 (mttm) REVERT: x 135 ASP cc_start: 0.7066 (m-30) cc_final: 0.6774 (m-30) REVERT: y 330 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (mmtm) REVERT: d 5 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5846 (mt0) REVERT: d 32 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8014 (ptm-80) REVERT: z 105 MET cc_start: 0.2768 (pmm) cc_final: 0.2266 (pmm) REVERT: z 178 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7637 (mp) REVERT: z 212 THR cc_start: 0.6794 (p) cc_final: 0.6584 (p) REVERT: k 226 LYS cc_start: 0.6782 (mttm) cc_final: 0.6399 (mmtm) REVERT: k 237 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7997 (mm) outliers start: 135 outliers final: 123 residues processed: 890 average time/residue: 0.8161 time to fit residues: 1221.4728 Evaluate side-chains 927 residues out of total 5134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 797 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 81 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 138 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain x residue 91 ASN Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 235 SER Chi-restraints excluded: chain y residue 22 ASP Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 308 MET Chi-restraints excluded: chain y residue 330 LYS Chi-restraints excluded: chain y residue 336 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 380 SER Chi-restraints excluded: chain d residue 5 GLN Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 114 GLN Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 93 SER Chi-restraints excluded: chain U residue 101 ILE Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 107 ASP Chi-restraints excluded: chain g residue 217 MET Chi-restraints excluded: chain g residue 222 ASN Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain z residue 118 ASN Chi-restraints excluded: chain z residue 178 ILE Chi-restraints excluded: chain z residue 193 ASN Chi-restraints excluded: chain z residue 238 ASN Chi-restraints excluded: chain z residue 276 VAL Chi-restraints excluded: chain z residue 277 MET Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 151 CYS Chi-restraints excluded: chain k residue 210 SER Chi-restraints excluded: chain k residue 237 LEU Chi-restraints excluded: chain k residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 468 optimal weight: 4.9990 chunk 628 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 544 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 591 optimal weight: 9.9990 chunk 247 optimal weight: 0.5980 chunk 607 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN I 7 ASN W 15 ASN X 63 ASN e 22 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 183 ASN z 273 HIS k 76 GLN ** k 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.168807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151466 restraints weight = 105865.580| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 0.95 r_work: 0.3451 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 85797 Z= 0.234 Angle : 0.606 15.526 123798 Z= 0.308 Chirality : 0.040 0.301 15303 Planarity : 0.004 0.089 9680 Dihedral : 22.872 179.069 32196 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 3.01 % Allowed : 20.52 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.96 (0.11), residues: 5844 helix: 0.56 (0.12), residues: 1842 sheet: -0.88 (0.17), residues: 991 loop : -1.30 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 82 HIS 0.008 0.001 HIS J 156 PHE 0.019 0.001 PHE x 96 TYR 0.018 0.001 TYR R 20 ARG 0.007 0.000 ARG I 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19788.29 seconds wall clock time: 348 minutes 9.31 seconds (20889.31 seconds total)