Starting phenix.real_space_refine on Wed Feb 14 04:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmv_10528/02_2024/6tmv_10528.pdb" } resolution = 3.45 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 36470 2.51 5 N 10176 2.21 5 O 11306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 221": "NH1" <-> "NH2" Residue "H ARG 255": "NH1" <-> "NH2" Residue "H PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 466": "OE1" <-> "OE2" Residue "I PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 221": "NH1" <-> "NH2" Residue "I ARG 255": "NH1" <-> "NH2" Residue "I PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 466": "OE1" <-> "OE2" Residue "I PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 221": "NH1" <-> "NH2" Residue "J ARG 255": "NH1" <-> "NH2" Residue "J PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 466": "OE1" <-> "OE2" Residue "J PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 255": "NH1" <-> "NH2" Residue "K PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 466": "OE1" <-> "OE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 221": "NH1" <-> "NH2" Residue "L ARG 255": "NH1" <-> "NH2" Residue "L PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 466": "OE1" <-> "OE2" Residue "M PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 221": "NH1" <-> "NH2" Residue "M ARG 255": "NH1" <-> "NH2" Residue "M PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 466": "OE1" <-> "OE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N ARG 255": "NH1" <-> "NH2" Residue "N PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 466": "OE1" <-> "OE2" Residue "N PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58106 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "K" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4163 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 529} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "M" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4141 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 21.69, per 1000 atoms: 0.37 Number of scatterers: 58106 At special positions: 0 Unit cell: (203.83, 188.57, 165.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 11306 8.00 N 10176 7.00 C 36470 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: 14.90 Conformation dependent library (CDL) restraints added in 8.0 seconds 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13980 Finding SS restraints... Secondary structure from input PDB file: 350 helices and 98 sheets defined 56.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.903A pdb=" N GLN A 13 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.512A pdb=" N SER A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.516A pdb=" N VAL A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 Processing helix chain 'A' and resid 107 through 129 removed outlier: 3.603A pdb=" N ASN A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.650A pdb=" N ALA A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.527A pdb=" N ALA A 201 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.504A pdb=" N LEU A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.791A pdb=" N THR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.712A pdb=" N GLN A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 345 through 365 removed outlier: 3.757A pdb=" N ARG A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 removed outlier: 3.509A pdb=" N PHE A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 373 through 387 Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.518A pdb=" N LYS A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.591A pdb=" N LYS A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.870A pdb=" N THR A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.603A pdb=" N LEU A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 523 through 542 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.848A pdb=" N GLN B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.550A pdb=" N SER B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 74 removed outlier: 4.131A pdb=" N VAL B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.545A pdb=" N HIS B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 129 removed outlier: 3.509A pdb=" N ASP B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.501A pdb=" N ALA B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.538A pdb=" N ALA B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 258 through 272 removed outlier: 3.797A pdb=" N THR B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL B 276 " --> pdb=" O PRO B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 276' Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.831A pdb=" N GLN B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 345 through 365 removed outlier: 3.762A pdb=" N ARG B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 removed outlier: 3.505A pdb=" N PHE B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 373 through 387 Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.595A pdb=" N LYS B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.521A pdb=" N SER B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.593A pdb=" N LEU B 498 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 523 through 542 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.854A pdb=" N GLN C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.570A pdb=" N SER C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.503A pdb=" N VAL C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 105 Processing helix chain 'C' and resid 107 through 129 removed outlier: 3.639A pdb=" N ASN C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.617A pdb=" N ALA C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.542A pdb=" N ALA C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 227 through 241 Processing helix chain 'C' and resid 258 through 272 removed outlier: 3.797A pdb=" N THR C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL C 276 " --> pdb=" O PRO C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.733A pdb=" N GLN C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 345 through 365 removed outlier: 3.753A pdb=" N ARG C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 removed outlier: 3.509A pdb=" N PHE C 372 " --> pdb=" O SER C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 400 through 423 removed outlier: 3.534A pdb=" N VAL C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.582A pdb=" N LYS C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.869A pdb=" N THR C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.594A pdb=" N LEU C 498 " --> pdb=" O ASP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 523 through 542 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.834A pdb=" N GLN D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 Processing helix chain 'D' and resid 63 through 74 removed outlier: 4.204A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 107 through 129 removed outlier: 3.521A pdb=" N ARG D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.539A pdb=" N ALA D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.553A pdb=" N ALA D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.796A pdb=" N THR D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 276 removed outlier: 3.512A pdb=" N VAL D 276 " --> pdb=" O PRO D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 273 through 276' Processing helix chain 'D' and resid 296 through 306 removed outlier: 3.829A pdb=" N GLN D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 345 through 365 removed outlier: 3.765A pdb=" N ARG D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 removed outlier: 3.505A pdb=" N PHE D 372 " --> pdb=" O SER D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 373 through 387 Processing helix chain 'D' and resid 400 through 423 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.535A pdb=" N LYS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.507A pdb=" N SER D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 495 through 499 removed outlier: 3.592A pdb=" N LEU D 498 " --> pdb=" O ASP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 542 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.833A pdb=" N GLN E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.568A pdb=" N SER E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 4.207A pdb=" N VAL E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 Processing helix chain 'E' and resid 107 through 129 removed outlier: 3.574A pdb=" N ASN E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 124 " --> pdb=" O ARG E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.634A pdb=" N ALA E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 removed outlier: 3.545A pdb=" N ALA E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 227 through 241 Processing helix chain 'E' and resid 258 through 272 removed outlier: 3.799A pdb=" N THR E 264 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 276 removed outlier: 3.515A pdb=" N VAL E 276 " --> pdb=" O PRO E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 296 through 306 removed outlier: 3.728A pdb=" N GLN E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 318 Processing helix chain 'E' and resid 345 through 365 removed outlier: 3.767A pdb=" N ARG E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 362 " --> pdb=" O GLY E 358 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 removed outlier: 3.513A pdb=" N PHE E 372 " --> pdb=" O SER E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 373 through 387 Processing helix chain 'E' and resid 400 through 423 removed outlier: 3.525A pdb=" N VAL E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 450 through 458 removed outlier: 3.586A pdb=" N LYS E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 removed outlier: 3.509A pdb=" N SER E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 472 " --> pdb=" O MET E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 495 through 499 removed outlier: 3.581A pdb=" N LEU E 498 " --> pdb=" O ASP E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 518 Processing helix chain 'E' and resid 523 through 542 removed outlier: 3.504A pdb=" N LEU E 530 " --> pdb=" O SER E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.787A pdb=" N GLN F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 Processing helix chain 'F' and resid 63 through 74 removed outlier: 4.202A pdb=" N VAL F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 105 removed outlier: 3.500A pdb=" N HIS F 100 " --> pdb=" O HIS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 129 removed outlier: 3.670A pdb=" N ASN F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.735A pdb=" N ARG F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 201 removed outlier: 3.539A pdb=" N ALA F 201 " --> pdb=" O PRO F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.502A pdb=" N LEU F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.796A pdb=" N THR F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 276 removed outlier: 3.506A pdb=" N VAL F 276 " --> pdb=" O PRO F 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 273 through 276' Processing helix chain 'F' and resid 296 through 306 removed outlier: 3.820A pdb=" N GLN F 300 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 318 Processing helix chain 'F' and resid 345 through 365 removed outlier: 3.757A pdb=" N ARG F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 362 " --> pdb=" O GLY F 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 365 " --> pdb=" O GLU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 removed outlier: 3.515A pdb=" N PHE F 372 " --> pdb=" O SER F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 373 through 387 Processing helix chain 'F' and resid 400 through 423 Processing helix chain 'F' and resid 431 through 447 Processing helix chain 'F' and resid 450 through 458 removed outlier: 3.529A pdb=" N LYS F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 removed outlier: 3.863A pdb=" N THR F 472 " --> pdb=" O MET F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 495 through 500 removed outlier: 4.221A pdb=" N ASN F 499 " --> pdb=" O ASP F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 522 through 542 Processing helix chain 'G' and resid 11 through 29 removed outlier: 3.559A pdb=" N LYS G 17 " --> pdb=" O GLN G 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.532A pdb=" N SER G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 removed outlier: 4.255A pdb=" N VAL G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 105 Processing helix chain 'G' and resid 107 through 129 removed outlier: 3.508A pdb=" N ASN G 113 " --> pdb=" O GLN G 109 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'G' and resid 150 through 164 removed outlier: 3.628A pdb=" N ALA G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 201 removed outlier: 3.537A pdb=" N ALA G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 226 No H-bonds generated for 'chain 'G' and resid 224 through 226' Processing helix chain 'G' and resid 227 through 241 Processing helix chain 'G' and resid 258 through 272 removed outlier: 3.795A pdb=" N THR G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 276 removed outlier: 3.508A pdb=" N VAL G 276 " --> pdb=" O PRO G 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.818A pdb=" N GLN G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 306 " --> pdb=" O ILE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 318 Processing helix chain 'G' and resid 345 through 365 removed outlier: 3.763A pdb=" N ARG G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 362 " --> pdb=" O GLY G 358 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY G 365 " --> pdb=" O GLU G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 removed outlier: 3.516A pdb=" N PHE G 372 " --> pdb=" O SER G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 373 through 387 Processing helix chain 'G' and resid 400 through 423 Processing helix chain 'G' and resid 431 through 447 Processing helix chain 'G' and resid 450 through 458 removed outlier: 3.570A pdb=" N LYS G 456 " --> pdb=" O ALA G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.807A pdb=" N THR G 472 " --> pdb=" O MET G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 Processing helix chain 'G' and resid 495 through 499 removed outlier: 3.609A pdb=" N LEU G 498 " --> pdb=" O ASP G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 518 Processing helix chain 'G' and resid 523 through 542 removed outlier: 3.516A pdb=" N LEU G 530 " --> pdb=" O SER G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.904A pdb=" N GLN H 13 " --> pdb=" O GLY H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.511A pdb=" N SER H 58 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 74 removed outlier: 3.516A pdb=" N VAL H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 105 Processing helix chain 'H' and resid 107 through 129 removed outlier: 3.604A pdb=" N ASN H 113 " --> pdb=" O GLN H 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 147 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.650A pdb=" N ALA H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 155 " --> pdb=" O GLU H 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 201 removed outlier: 3.526A pdb=" N ALA H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'H' and resid 227 through 241 removed outlier: 3.505A pdb=" N LEU H 238 " --> pdb=" O GLY H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 272 removed outlier: 3.792A pdb=" N THR H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL H 276 " --> pdb=" O PRO H 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 273 through 276' Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.711A pdb=" N GLN H 300 " --> pdb=" O THR H 296 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 306 " --> pdb=" O ILE H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 318 Processing helix chain 'H' and resid 345 through 365 removed outlier: 3.757A pdb=" N ARG H 351 " --> pdb=" O LYS H 347 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 362 " --> pdb=" O GLY H 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY H 365 " --> pdb=" O GLU H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 372 removed outlier: 3.509A pdb=" N PHE H 372 " --> pdb=" O SER H 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 369 through 372' Processing helix chain 'H' and resid 373 through 387 Processing helix chain 'H' and resid 400 through 423 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.518A pdb=" N LYS H 442 " --> pdb=" O PHE H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 458 removed outlier: 3.591A pdb=" N LYS H 456 " --> pdb=" O ALA H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 472 removed outlier: 3.870A pdb=" N THR H 472 " --> pdb=" O MET H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 479 Processing helix chain 'H' and resid 495 through 499 removed outlier: 3.604A pdb=" N LEU H 498 " --> pdb=" O ASP H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 518 Processing helix chain 'H' and resid 523 through 542 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.848A pdb=" N GLN I 13 " --> pdb=" O GLY I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.549A pdb=" N SER I 58 " --> pdb=" O THR I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 4.132A pdb=" N VAL I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 105 removed outlier: 3.544A pdb=" N HIS I 100 " --> pdb=" O HIS I 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 129 removed outlier: 3.511A pdb=" N ASP I 116 " --> pdb=" O ARG I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 147 Processing helix chain 'I' and resid 150 through 164 removed outlier: 3.501A pdb=" N ALA I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 3.538A pdb=" N ALA I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 226 No H-bonds generated for 'chain 'I' and resid 224 through 226' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 258 through 272 removed outlier: 3.796A pdb=" N THR I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL I 276 " --> pdb=" O PRO I 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 273 through 276' Processing helix chain 'I' and resid 296 through 306 removed outlier: 3.831A pdb=" N GLN I 300 " --> pdb=" O THR I 296 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 306 " --> pdb=" O ILE I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 318 Processing helix chain 'I' and resid 345 through 365 removed outlier: 3.762A pdb=" N ARG I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 362 " --> pdb=" O GLY I 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY I 365 " --> pdb=" O GLU I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 372 removed outlier: 3.505A pdb=" N PHE I 372 " --> pdb=" O SER I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 369 through 372' Processing helix chain 'I' and resid 373 through 387 Processing helix chain 'I' and resid 400 through 423 Processing helix chain 'I' and resid 431 through 447 Processing helix chain 'I' and resid 450 through 458 removed outlier: 3.594A pdb=" N LYS I 456 " --> pdb=" O ALA I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 472 removed outlier: 3.521A pdb=" N SER I 471 " --> pdb=" O LEU I 467 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR I 472 " --> pdb=" O MET I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 479 Processing helix chain 'I' and resid 495 through 499 removed outlier: 3.594A pdb=" N LEU I 498 " --> pdb=" O ASP I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 Processing helix chain 'I' and resid 523 through 542 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.853A pdb=" N GLN J 13 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.571A pdb=" N SER J 58 " --> pdb=" O THR J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 removed outlier: 3.503A pdb=" N VAL J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 105 Processing helix chain 'J' and resid 107 through 129 removed outlier: 3.640A pdb=" N ASN J 113 " --> pdb=" O GLN J 109 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP J 116 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG J 124 " --> pdb=" O ARG J 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 147 Processing helix chain 'J' and resid 150 through 164 removed outlier: 3.617A pdb=" N ALA J 154 " --> pdb=" O ASP J 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN J 164 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.542A pdb=" N ALA J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 226 No H-bonds generated for 'chain 'J' and resid 224 through 226' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 258 through 272 removed outlier: 3.797A pdb=" N THR J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL J 276 " --> pdb=" O PRO J 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 273 through 276' Processing helix chain 'J' and resid 296 through 306 removed outlier: 3.734A pdb=" N GLN J 300 " --> pdb=" O THR J 296 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 306 " --> pdb=" O ILE J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 318 Processing helix chain 'J' and resid 345 through 365 removed outlier: 3.753A pdb=" N ARG J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU J 362 " --> pdb=" O GLY J 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 365 " --> pdb=" O GLU J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 372 removed outlier: 3.509A pdb=" N PHE J 372 " --> pdb=" O SER J 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 369 through 372' Processing helix chain 'J' and resid 373 through 387 Processing helix chain 'J' and resid 400 through 423 removed outlier: 3.532A pdb=" N VAL J 413 " --> pdb=" O ARG J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 447 Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.582A pdb=" N LYS J 456 " --> pdb=" O ALA J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 472 removed outlier: 3.868A pdb=" N THR J 472 " --> pdb=" O MET J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 479 Processing helix chain 'J' and resid 495 through 499 removed outlier: 3.594A pdb=" N LEU J 498 " --> pdb=" O ASP J 495 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 518 Processing helix chain 'J' and resid 523 through 542 Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.833A pdb=" N GLN K 13 " --> pdb=" O GLY K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 57 Processing helix chain 'K' and resid 63 through 74 removed outlier: 4.204A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 105 Processing helix chain 'K' and resid 107 through 129 removed outlier: 3.519A pdb=" N ARG K 112 " --> pdb=" O PHE K 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN K 113 " --> pdb=" O GLN K 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP K 116 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 147 Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.538A pdb=" N ALA K 154 " --> pdb=" O ASP K 150 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG K 155 " --> pdb=" O GLU K 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 201 removed outlier: 3.554A pdb=" N ALA K 201 " --> pdb=" O PRO K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 258 through 272 removed outlier: 3.795A pdb=" N THR K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 276 removed outlier: 3.511A pdb=" N VAL K 276 " --> pdb=" O PRO K 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 273 through 276' Processing helix chain 'K' and resid 296 through 306 removed outlier: 3.829A pdb=" N GLN K 300 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K 306 " --> pdb=" O ILE K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 318 Processing helix chain 'K' and resid 345 through 365 removed outlier: 3.765A pdb=" N ARG K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 362 " --> pdb=" O GLY K 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY K 365 " --> pdb=" O GLU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 372 removed outlier: 3.507A pdb=" N PHE K 372 " --> pdb=" O SER K 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 369 through 372' Processing helix chain 'K' and resid 373 through 387 Processing helix chain 'K' and resid 400 through 423 Processing helix chain 'K' and resid 431 through 447 Processing helix chain 'K' and resid 450 through 458 removed outlier: 3.534A pdb=" N LYS K 456 " --> pdb=" O ALA K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 472 removed outlier: 3.508A pdb=" N SER K 471 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR K 472 " --> pdb=" O MET K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 472 through 479 Processing helix chain 'K' and resid 495 through 499 removed outlier: 3.592A pdb=" N LEU K 498 " --> pdb=" O ASP K 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 518 Processing helix chain 'K' and resid 522 through 542 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.832A pdb=" N GLN L 13 " --> pdb=" O GLY L 9 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 59 removed outlier: 3.569A pdb=" N SER L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 74 removed outlier: 4.206A pdb=" N VAL L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 105 Processing helix chain 'L' and resid 107 through 129 removed outlier: 3.575A pdb=" N ASN L 113 " --> pdb=" O GLN L 109 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP L 116 " --> pdb=" O ARG L 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG L 124 " --> pdb=" O ARG L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 147 Processing helix chain 'L' and resid 150 through 164 removed outlier: 3.634A pdb=" N ALA L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG L 155 " --> pdb=" O GLU L 151 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN L 164 " --> pdb=" O LEU L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 removed outlier: 3.545A pdb=" N ALA L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 226 No H-bonds generated for 'chain 'L' and resid 224 through 226' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 258 through 272 removed outlier: 3.799A pdb=" N THR L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN L 267 " --> pdb=" O SER L 263 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 276 removed outlier: 3.515A pdb=" N VAL L 276 " --> pdb=" O PRO L 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 273 through 276' Processing helix chain 'L' and resid 296 through 306 removed outlier: 3.728A pdb=" N GLN L 300 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 306 " --> pdb=" O ILE L 302 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 318 Processing helix chain 'L' and resid 345 through 365 removed outlier: 3.767A pdb=" N ARG L 351 " --> pdb=" O LYS L 347 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU L 362 " --> pdb=" O GLY L 358 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY L 365 " --> pdb=" O GLU L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 372 removed outlier: 3.513A pdb=" N PHE L 372 " --> pdb=" O SER L 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 369 through 372' Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 400 through 423 removed outlier: 3.525A pdb=" N VAL L 413 " --> pdb=" O ARG L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 447 Processing helix chain 'L' and resid 450 through 458 removed outlier: 3.586A pdb=" N LYS L 456 " --> pdb=" O ALA L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 472 removed outlier: 3.510A pdb=" N SER L 471 " --> pdb=" O LEU L 467 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR L 472 " --> pdb=" O MET L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 479 Processing helix chain 'L' and resid 495 through 499 removed outlier: 3.582A pdb=" N LEU L 498 " --> pdb=" O ASP L 495 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 518 Processing helix chain 'L' and resid 523 through 542 removed outlier: 3.505A pdb=" N LEU L 530 " --> pdb=" O SER L 526 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.787A pdb=" N GLN M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 59 Processing helix chain 'M' and resid 63 through 74 removed outlier: 4.202A pdb=" N VAL M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 105 Processing helix chain 'M' and resid 107 through 129 removed outlier: 3.671A pdb=" N ASN M 113 " --> pdb=" O GLN M 109 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER M 127 " --> pdb=" O GLN M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 147 Processing helix chain 'M' and resid 150 through 164 removed outlier: 3.736A pdb=" N ARG M 155 " --> pdb=" O GLU M 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN M 164 " --> pdb=" O LEU M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 201 removed outlier: 3.539A pdb=" N ALA M 201 " --> pdb=" O PRO M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 227 through 241 removed outlier: 3.502A pdb=" N LEU M 238 " --> pdb=" O GLY M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 272 removed outlier: 3.796A pdb=" N THR M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS M 272 " --> pdb=" O LEU M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 276 removed outlier: 3.505A pdb=" N VAL M 276 " --> pdb=" O PRO M 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 273 through 276' Processing helix chain 'M' and resid 296 through 306 removed outlier: 3.820A pdb=" N GLN M 300 " --> pdb=" O THR M 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 306 " --> pdb=" O ILE M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 318 Processing helix chain 'M' and resid 345 through 365 removed outlier: 3.758A pdb=" N ARG M 351 " --> pdb=" O LYS M 347 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU M 362 " --> pdb=" O GLY M 358 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY M 365 " --> pdb=" O GLU M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 372 removed outlier: 3.514A pdb=" N PHE M 372 " --> pdb=" O SER M 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 369 through 372' Processing helix chain 'M' and resid 373 through 387 Processing helix chain 'M' and resid 400 through 423 Processing helix chain 'M' and resid 431 through 447 Processing helix chain 'M' and resid 450 through 458 removed outlier: 3.530A pdb=" N LYS M 456 " --> pdb=" O ALA M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 462 through 472 removed outlier: 3.864A pdb=" N THR M 472 " --> pdb=" O MET M 468 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 479 Processing helix chain 'M' and resid 495 through 500 removed outlier: 4.223A pdb=" N ASN M 499 " --> pdb=" O ASP M 495 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 518 Processing helix chain 'M' and resid 522 through 542 Processing helix chain 'N' and resid 11 through 29 removed outlier: 3.559A pdb=" N LYS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 59 removed outlier: 3.533A pdb=" N SER N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 74 removed outlier: 4.254A pdb=" N VAL N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE N 73 " --> pdb=" O VAL N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 105 Processing helix chain 'N' and resid 107 through 129 removed outlier: 3.508A pdb=" N ASN N 113 " --> pdb=" O GLN N 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP N 116 " --> pdb=" O ARG N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 147 Processing helix chain 'N' and resid 150 through 164 removed outlier: 3.628A pdb=" N ALA N 154 " --> pdb=" O ASP N 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG N 155 " --> pdb=" O GLU N 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN N 164 " --> pdb=" O LEU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 201 removed outlier: 3.537A pdb=" N ALA N 201 " --> pdb=" O PRO N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 226 No H-bonds generated for 'chain 'N' and resid 224 through 226' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 258 through 272 removed outlier: 3.795A pdb=" N THR N 264 " --> pdb=" O ALA N 260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS N 272 " --> pdb=" O LEU N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 276 removed outlier: 3.508A pdb=" N VAL N 276 " --> pdb=" O PRO N 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 273 through 276' Processing helix chain 'N' and resid 296 through 306 removed outlier: 3.819A pdb=" N GLN N 300 " --> pdb=" O THR N 296 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 306 " --> pdb=" O ILE N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 318 Processing helix chain 'N' and resid 345 through 365 removed outlier: 3.763A pdb=" N ARG N 351 " --> pdb=" O LYS N 347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 362 " --> pdb=" O GLY N 358 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY N 365 " --> pdb=" O GLU N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 372 removed outlier: 3.516A pdb=" N PHE N 372 " --> pdb=" O SER N 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 369 through 372' Processing helix chain 'N' and resid 373 through 387 Processing helix chain 'N' and resid 400 through 423 Processing helix chain 'N' and resid 431 through 447 Processing helix chain 'N' and resid 450 through 458 removed outlier: 3.570A pdb=" N LYS N 456 " --> pdb=" O ALA N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 462 through 472 removed outlier: 3.806A pdb=" N THR N 472 " --> pdb=" O MET N 468 " (cutoff:3.500A) Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'N' and resid 495 through 499 removed outlier: 3.609A pdb=" N LEU N 498 " --> pdb=" O ASP N 495 " (cutoff:3.500A) Processing helix chain 'N' and resid 513 through 518 Processing helix chain 'N' and resid 523 through 542 removed outlier: 3.516A pdb=" N LEU N 530 " --> pdb=" O SER N 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 4.664A pdb=" N THR A 543 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N MET B 39 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 545 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS B 41 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 547 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN B 42 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 3.555A pdb=" N ASN A 42 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 37 " --> pdb=" O THR G 543 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR G 545 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.220A pdb=" N ASP A 170 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 393 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 172 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 395 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 174 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 removed outlier: 6.820A pdb=" N ILE A 250 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 286 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 252 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU A 311 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 218 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 427 Processing sheet with id=AA8, first strand: chain 'A' and resid 503 through 505 removed outlier: 3.768A pdb=" N GLY A 512 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 510 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 8 removed outlier: 4.610A pdb=" N THR B 543 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N MET C 39 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 545 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS C 41 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE B 547 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 42 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 190 through 191 Processing sheet with id=AB3, first strand: chain 'B' and resid 194 through 195 removed outlier: 8.976A pdb=" N LEU B 311 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 218 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AB5, first strand: chain 'B' and resid 425 through 427 Processing sheet with id=AB6, first strand: chain 'B' and resid 503 through 505 removed outlier: 3.821A pdb=" N GLY B 512 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 510 " --> pdb=" O ASN B 505 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 8 removed outlier: 4.672A pdb=" N THR C 543 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N MET D 39 " --> pdb=" O THR C 543 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C 545 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS D 41 " --> pdb=" O THR C 545 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 547 " --> pdb=" O LYS D 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN D 42 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.216A pdb=" N ASP C 170 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE C 393 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C 172 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 395 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS C 174 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.403A pdb=" N GLN C 331 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 195 removed outlier: 8.968A pdb=" N LEU C 311 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 218 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AC3, first strand: chain 'C' and resid 425 through 427 Processing sheet with id=AC4, first strand: chain 'C' and resid 503 through 505 removed outlier: 3.775A pdb=" N GLY C 512 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 510 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.615A pdb=" N THR D 543 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N MET E 39 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 545 " --> pdb=" O MET E 39 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LYS E 41 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE D 547 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 42 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 170 through 175 removed outlier: 6.342A pdb=" N ASP D 170 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 393 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU D 172 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL D 395 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS D 174 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 190 through 191 Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 195 removed outlier: 8.980A pdb=" N LEU D 311 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 218 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AD1, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AD2, first strand: chain 'D' and resid 503 through 505 removed outlier: 3.808A pdb=" N GLY D 512 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 510 " --> pdb=" O ASN D 505 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 6 through 8 removed outlier: 4.735A pdb=" N THR E 543 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET F 39 " --> pdb=" O THR E 543 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR E 545 " --> pdb=" O MET F 39 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LYS F 41 " --> pdb=" O THR E 545 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 547 " --> pdb=" O LYS F 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN F 42 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 170 through 175 removed outlier: 6.204A pdb=" N ASP E 170 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE E 393 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU E 172 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL E 395 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS E 174 " --> pdb=" O VAL E 395 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 190 through 191 Processing sheet with id=AD6, first strand: chain 'E' and resid 194 through 195 removed outlier: 8.970A pdb=" N LEU E 311 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 218 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 222 through 223 Processing sheet with id=AD8, first strand: chain 'E' and resid 425 through 427 Processing sheet with id=AD9, first strand: chain 'E' and resid 503 through 505 removed outlier: 3.792A pdb=" N GLY E 512 " --> pdb=" O VAL E 503 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 510 " --> pdb=" O ASN E 505 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 6 through 8 removed outlier: 5.920A pdb=" N LEU G 37 " --> pdb=" O THR F 543 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 545 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 170 through 175 Processing sheet with id=AE3, first strand: chain 'F' and resid 190 through 191 Processing sheet with id=AE4, first strand: chain 'F' and resid 194 through 195 removed outlier: 8.982A pdb=" N LEU F 311 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 218 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AE6, first strand: chain 'F' and resid 426 through 427 Processing sheet with id=AE7, first strand: chain 'F' and resid 503 through 505 removed outlier: 3.881A pdb=" N GLY F 512 " --> pdb=" O VAL F 503 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 510 " --> pdb=" O ASN F 505 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 168 through 175 removed outlier: 3.844A pdb=" N LYS G 389 " --> pdb=" O TYR G 168 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 189 through 191 Processing sheet with id=AF1, first strand: chain 'G' and resid 194 through 195 removed outlier: 8.986A pdb=" N LEU G 311 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 218 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AF3, first strand: chain 'G' and resid 425 through 427 Processing sheet with id=AF4, first strand: chain 'G' and resid 503 through 505 removed outlier: 3.819A pdb=" N GLY G 512 " --> pdb=" O VAL G 503 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU G 510 " --> pdb=" O ASN G 505 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 6 through 8 removed outlier: 4.666A pdb=" N THR H 543 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET I 39 " --> pdb=" O THR H 543 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR H 545 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS I 41 " --> pdb=" O THR H 545 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE H 547 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN I 42 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 45 through 49 removed outlier: 3.555A pdb=" N ASN H 42 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU H 37 " --> pdb=" O THR N 543 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR N 545 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 170 through 175 removed outlier: 6.220A pdb=" N ASP H 170 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE H 393 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU H 172 " --> pdb=" O ILE H 393 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL H 395 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS H 174 " --> pdb=" O VAL H 395 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 190 through 191 Processing sheet with id=AF9, first strand: chain 'H' and resid 194 through 195 removed outlier: 8.973A pdb=" N LEU H 311 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL H 218 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 222 through 223 Processing sheet with id=AG2, first strand: chain 'H' and resid 425 through 427 Processing sheet with id=AG3, first strand: chain 'H' and resid 503 through 505 removed outlier: 3.769A pdb=" N GLY H 512 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU H 510 " --> pdb=" O ASN H 505 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 6 through 8 removed outlier: 4.612A pdb=" N THR I 543 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N MET J 39 " --> pdb=" O THR I 543 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR I 545 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS J 41 " --> pdb=" O THR I 545 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE I 547 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN J 42 " --> pdb=" O SER J 45 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 170 through 175 Processing sheet with id=AG6, first strand: chain 'I' and resid 190 through 191 Processing sheet with id=AG7, first strand: chain 'I' and resid 194 through 195 removed outlier: 8.976A pdb=" N LEU I 311 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL I 218 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 222 through 223 Processing sheet with id=AG9, first strand: chain 'I' and resid 425 through 427 Processing sheet with id=AH1, first strand: chain 'I' and resid 503 through 505 removed outlier: 3.822A pdb=" N GLY I 512 " --> pdb=" O VAL I 503 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU I 510 " --> pdb=" O ASN I 505 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 6 through 8 removed outlier: 4.675A pdb=" N THR J 543 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N MET K 39 " --> pdb=" O THR J 543 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR J 545 " --> pdb=" O MET K 39 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LYS K 41 " --> pdb=" O THR J 545 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE J 547 " --> pdb=" O LYS K 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN K 42 " --> pdb=" O SER K 45 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 170 through 175 removed outlier: 6.216A pdb=" N ASP J 170 " --> pdb=" O ILE J 391 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE J 393 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU J 172 " --> pdb=" O ILE J 393 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL J 395 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS J 174 " --> pdb=" O VAL J 395 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 190 through 191 removed outlier: 6.402A pdb=" N GLN J 331 " --> pdb=" O LYS J 342 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 194 through 195 removed outlier: 8.969A pdb=" N LEU J 311 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL J 218 " --> pdb=" O LEU J 311 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 222 through 223 Processing sheet with id=AH7, first strand: chain 'J' and resid 425 through 427 Processing sheet with id=AH8, first strand: chain 'J' and resid 503 through 505 removed outlier: 3.775A pdb=" N GLY J 512 " --> pdb=" O VAL J 503 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU J 510 " --> pdb=" O ASN J 505 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 6 through 8 removed outlier: 4.618A pdb=" N THR K 543 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET L 39 " --> pdb=" O THR K 543 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR K 545 " --> pdb=" O MET L 39 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS L 41 " --> pdb=" O THR K 545 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE K 547 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN L 42 " --> pdb=" O SER L 45 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 170 through 175 removed outlier: 6.342A pdb=" N ASP K 170 " --> pdb=" O ILE K 391 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE K 393 " --> pdb=" O ASP K 170 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU K 172 " --> pdb=" O ILE K 393 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL K 395 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS K 174 " --> pdb=" O VAL K 395 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 190 through 191 Processing sheet with id=AI3, first strand: chain 'K' and resid 194 through 195 removed outlier: 8.981A pdb=" N LEU K 311 " --> pdb=" O ALA K 216 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL K 218 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 222 through 223 Processing sheet with id=AI5, first strand: chain 'K' and resid 426 through 427 Processing sheet with id=AI6, first strand: chain 'K' and resid 503 through 505 removed outlier: 3.809A pdb=" N GLY K 512 " --> pdb=" O VAL K 503 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU K 510 " --> pdb=" O ASN K 505 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 6 through 8 removed outlier: 4.737A pdb=" N THR L 543 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N MET M 39 " --> pdb=" O THR L 543 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR L 545 " --> pdb=" O MET M 39 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS M 41 " --> pdb=" O THR L 545 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE L 547 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN M 42 " --> pdb=" O SER M 45 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 170 through 175 removed outlier: 6.203A pdb=" N ASP L 170 " --> pdb=" O ILE L 391 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE L 393 " --> pdb=" O ASP L 170 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU L 172 " --> pdb=" O ILE L 393 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL L 395 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS L 174 " --> pdb=" O VAL L 395 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 190 through 191 Processing sheet with id=AJ1, first strand: chain 'L' and resid 194 through 195 removed outlier: 8.970A pdb=" N LEU L 311 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL L 218 " --> pdb=" O LEU L 311 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 222 through 223 Processing sheet with id=AJ3, first strand: chain 'L' and resid 425 through 427 Processing sheet with id=AJ4, first strand: chain 'L' and resid 503 through 505 removed outlier: 3.791A pdb=" N GLY L 512 " --> pdb=" O VAL L 503 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU L 510 " --> pdb=" O ASN L 505 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 6 through 8 removed outlier: 5.913A pdb=" N LEU N 37 " --> pdb=" O THR M 543 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR M 545 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 170 through 175 Processing sheet with id=AJ7, first strand: chain 'M' and resid 190 through 191 Processing sheet with id=AJ8, first strand: chain 'M' and resid 194 through 195 removed outlier: 8.983A pdb=" N LEU M 311 " --> pdb=" O ALA M 216 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL M 218 " --> pdb=" O LEU M 311 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 222 through 223 Processing sheet with id=AK1, first strand: chain 'M' and resid 426 through 427 Processing sheet with id=AK2, first strand: chain 'M' and resid 503 through 505 removed outlier: 3.881A pdb=" N GLY M 512 " --> pdb=" O VAL M 503 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU M 510 " --> pdb=" O ASN M 505 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 168 through 175 removed outlier: 3.845A pdb=" N LYS N 389 " --> pdb=" O TYR N 168 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'N' and resid 189 through 191 Processing sheet with id=AK5, first strand: chain 'N' and resid 194 through 195 removed outlier: 8.986A pdb=" N LEU N 311 " --> pdb=" O ALA N 216 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL N 218 " --> pdb=" O LEU N 311 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 222 through 223 Processing sheet with id=AK7, first strand: chain 'N' and resid 425 through 427 Processing sheet with id=AK8, first strand: chain 'N' and resid 503 through 505 removed outlier: 3.818A pdb=" N GLY N 512 " --> pdb=" O VAL N 503 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU N 510 " --> pdb=" O ASN N 505 " (cutoff:3.500A) 3122 hydrogen bonds defined for protein. 8904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.52 Time building geometry restraints manager: 16.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19646 1.34 - 1.46: 5545 1.46 - 1.58: 33537 1.58 - 1.70: 0 1.70 - 1.81: 294 Bond restraints: 59022 Sorted by residual: bond pdb=" CA ILE M 284 " pdb=" CB ILE M 284 " ideal model delta sigma weight residual 1.539 1.562 -0.023 7.50e-03 1.78e+04 9.12e+00 bond pdb=" CA ILE D 284 " pdb=" CB ILE D 284 " ideal model delta sigma weight residual 1.539 1.562 -0.023 7.50e-03 1.78e+04 9.05e+00 bond pdb=" CA ILE A 284 " pdb=" CB ILE A 284 " ideal model delta sigma weight residual 1.539 1.561 -0.022 7.50e-03 1.78e+04 8.68e+00 bond pdb=" CA ILE I 284 " pdb=" CB ILE I 284 " ideal model delta sigma weight residual 1.539 1.561 -0.022 7.50e-03 1.78e+04 8.67e+00 bond pdb=" CA ILE G 284 " pdb=" CB ILE G 284 " ideal model delta sigma weight residual 1.539 1.561 -0.022 7.50e-03 1.78e+04 8.60e+00 ... (remaining 59017 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.13: 1300 107.13 - 113.91: 32449 113.91 - 120.68: 24364 120.68 - 127.46: 21561 127.46 - 134.24: 392 Bond angle restraints: 80066 Sorted by residual: angle pdb=" N ILE L 473 " pdb=" CA ILE L 473 " pdb=" C ILE L 473 " ideal model delta sigma weight residual 110.36 116.54 -6.18 1.05e+00 9.07e-01 3.46e+01 angle pdb=" N ILE E 473 " pdb=" CA ILE E 473 " pdb=" C ILE E 473 " ideal model delta sigma weight residual 110.36 116.49 -6.13 1.05e+00 9.07e-01 3.40e+01 angle pdb=" N ILE M 473 " pdb=" CA ILE M 473 " pdb=" C ILE M 473 " ideal model delta sigma weight residual 110.36 115.89 -5.53 1.05e+00 9.07e-01 2.77e+01 angle pdb=" N ILE F 473 " pdb=" CA ILE F 473 " pdb=" C ILE F 473 " ideal model delta sigma weight residual 110.36 115.82 -5.46 1.05e+00 9.07e-01 2.70e+01 angle pdb=" N ILE J 473 " pdb=" CA ILE J 473 " pdb=" C ILE J 473 " ideal model delta sigma weight residual 110.36 115.74 -5.38 1.05e+00 9.07e-01 2.63e+01 ... (remaining 80061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 31813 16.35 - 32.70: 2819 32.70 - 49.05: 609 49.05 - 65.41: 213 65.41 - 81.76: 34 Dihedral angle restraints: 35488 sinusoidal: 13744 harmonic: 21744 Sorted by residual: dihedral pdb=" CA ALA A 293 " pdb=" C ALA A 293 " pdb=" N ILE A 294 " pdb=" CA ILE A 294 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA H 293 " pdb=" C ALA H 293 " pdb=" N ILE H 294 " pdb=" CA ILE H 294 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C THR H 542 " pdb=" N THR H 542 " pdb=" CA THR H 542 " pdb=" CB THR H 542 " ideal model delta harmonic sigma weight residual -122.00 -131.07 9.07 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 35485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 6248 0.059 - 0.118: 2589 0.118 - 0.177: 489 0.177 - 0.237: 96 0.237 - 0.296: 30 Chirality restraints: 9452 Sorted by residual: chirality pdb=" CA THR H 542 " pdb=" N THR H 542 " pdb=" C THR H 542 " pdb=" CB THR H 542 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA THR A 542 " pdb=" N THR A 542 " pdb=" C THR A 542 " pdb=" CB THR A 542 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA GLU H 75 " pdb=" N GLU H 75 " pdb=" C GLU H 75 " pdb=" CB GLU H 75 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 9449 not shown) Planarity restraints: 10410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 75 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO I 76 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 75 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO B 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 75 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO F 76 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 10407 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 26740 3.05 - 3.51: 58816 3.51 - 3.97: 90005 3.97 - 4.44: 98035 4.44 - 4.90: 166934 Nonbonded interactions: 440530 Sorted by model distance: nonbonded pdb=" O TYR F 24 " pdb=" OG1 THR F 28 " model vdw 2.584 2.440 nonbonded pdb=" O TYR M 24 " pdb=" OG1 THR M 28 " model vdw 2.585 2.440 nonbonded pdb=" O ALA N 436 " pdb=" OG1 THR N 440 " model vdw 2.585 2.440 nonbonded pdb=" O ALA G 436 " pdb=" OG1 THR G 440 " model vdw 2.586 2.440 nonbonded pdb=" O ILE J 294 " pdb=" OH TYR J 378 " model vdw 2.586 2.440 ... (remaining 440525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'B' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'C' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'D' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'E' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'F' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'G' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'H' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'I' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'J' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'K' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'L' and (resid 4 through 289 or resid 295 through 299 or (resid 300 and ( \ name N or name CA or name C or name O or name CB )) or resid 301 through 549)) selection = (chain 'M' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) selection = (chain 'N' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name N or \ name CA or name C or name O or name CB )) or resid 382 through 549)) } 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.780 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 114.230 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.180 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.008 0.038 59022 Z= 0.509 Angle : 1.291 9.634 80066 Z= 0.861 Chirality : 0.066 0.296 9452 Planarity : 0.004 0.052 10410 Dihedral : 13.720 81.757 21508 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.04 % Allowed : 5.06 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.08), residues: 7560 helix: -1.99 (0.06), residues: 3906 sheet: -2.16 (0.15), residues: 840 loop : -1.90 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 497 HIS 0.005 0.001 HIS M 475 PHE 0.015 0.002 PHE G 438 TYR 0.013 0.002 TYR K 99 ARG 0.003 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1030 time to evaluate : 4.703 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: A 11 ASP cc_start: 0.8241 (m-30) cc_final: 0.7775 (t0) REVERT: A 39 MET cc_start: 0.9025 (ttm) cc_final: 0.8765 (ttm) REVERT: A 44 VAL cc_start: 0.8634 (m) cc_final: 0.8357 (t) REVERT: A 418 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7428 (ttm-80) REVERT: A 465 ASN cc_start: 0.8792 (t0) cc_final: 0.8489 (t0) REVERT: A 495 ASP cc_start: 0.8777 (t0) cc_final: 0.8514 (m-30) REVERT: A 508 THR cc_start: 0.7490 (m) cc_final: 0.7245 (p) REVERT: B 155 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8100 (mmm160) REVERT: B 184 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7523 (tm-30) REVERT: B 360 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6340 (tp30) REVERT: B 364 GLU cc_start: 0.8519 (tt0) cc_final: 0.8120 (mp0) REVERT: B 446 GLU cc_start: 0.8328 (tt0) cc_final: 0.8051 (tm-30) REVERT: C 10 LYS cc_start: 0.8522 (mttt) cc_final: 0.7892 (mmtm) REVERT: C 11 ASP cc_start: 0.8025 (m-30) cc_final: 0.7609 (t0) REVERT: C 170 ASP cc_start: 0.7452 (t70) cc_final: 0.7014 (t0) REVERT: C 255 ARG cc_start: 0.3537 (tpp80) cc_final: 0.3208 (ttm170) REVERT: C 340 ILE cc_start: 0.6092 (mt) cc_final: 0.5836 (tt) REVERT: C 446 GLU cc_start: 0.7628 (tt0) cc_final: 0.7344 (tp30) REVERT: D 10 LYS cc_start: 0.8206 (mttt) cc_final: 0.7600 (tppt) REVERT: D 44 VAL cc_start: 0.8924 (m) cc_final: 0.8615 (t) REVERT: D 119 GLU cc_start: 0.8549 (tp30) cc_final: 0.8213 (tm-30) REVERT: D 140 TYR cc_start: 0.6819 (t80) cc_final: 0.6497 (t80) REVERT: D 155 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7670 (tpm170) REVERT: D 178 ASN cc_start: 0.6439 (m110) cc_final: 0.5909 (t0) REVERT: D 301 ASP cc_start: 0.5976 (m-30) cc_final: 0.5678 (m-30) REVERT: D 305 MET cc_start: 0.7687 (mtt) cc_final: 0.7404 (mtt) REVERT: D 338 ARG cc_start: 0.6686 (ptt-90) cc_final: 0.6174 (pmt-80) REVERT: D 340 ILE cc_start: 0.7779 (mt) cc_final: 0.7151 (mp) REVERT: D 496 ASP cc_start: 0.8683 (t70) cc_final: 0.8162 (m-30) REVERT: D 504 MET cc_start: 0.7468 (ttm) cc_final: 0.7047 (ttm) REVERT: E 116 ASP cc_start: 0.8424 (t0) cc_final: 0.7972 (m-30) REVERT: E 145 THR cc_start: 0.8574 (m) cc_final: 0.8345 (p) REVERT: E 285 PRO cc_start: 0.4497 (Cg_exo) cc_final: 0.4162 (Cg_endo) REVERT: E 410 TYR cc_start: 0.7247 (m-80) cc_final: 0.6633 (m-80) REVERT: E 442 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7952 (ttpp) REVERT: E 446 GLU cc_start: 0.7548 (tt0) cc_final: 0.7206 (pp20) REVERT: E 476 LYS cc_start: 0.8769 (tttt) cc_final: 0.8385 (ttmt) REVERT: F 10 LYS cc_start: 0.8684 (mttt) cc_final: 0.8288 (pttm) REVERT: F 38 VAL cc_start: 0.9246 (t) cc_final: 0.8987 (p) REVERT: F 116 ASP cc_start: 0.8517 (t0) cc_final: 0.8232 (m-30) REVERT: F 119 GLU cc_start: 0.8593 (tp30) cc_final: 0.7889 (tp30) REVERT: F 191 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6832 (mp) REVERT: F 340 ILE cc_start: 0.6628 (mt) cc_final: 0.6139 (tt) REVERT: G 299 LEU cc_start: 0.5166 (mt) cc_final: 0.4754 (mp) REVERT: G 334 LEU cc_start: 0.7003 (mt) cc_final: 0.6571 (tp) REVERT: G 418 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7528 (mmm160) REVERT: G 488 ASN cc_start: 0.6691 (p0) cc_final: 0.6331 (p0) REVERT: H 11 ASP cc_start: 0.8241 (m-30) cc_final: 0.7791 (t0) REVERT: H 39 MET cc_start: 0.9021 (ttm) cc_final: 0.8748 (ttm) REVERT: H 44 VAL cc_start: 0.8652 (m) cc_final: 0.8381 (t) REVERT: H 191 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.5891 (pt) REVERT: H 418 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7565 (ttm-80) REVERT: H 465 ASN cc_start: 0.8776 (t0) cc_final: 0.8481 (t0) REVERT: H 476 LYS cc_start: 0.8884 (tttt) cc_final: 0.8683 (ttmt) REVERT: H 495 ASP cc_start: 0.8781 (t0) cc_final: 0.8510 (m-30) REVERT: H 508 THR cc_start: 0.7481 (m) cc_final: 0.7233 (p) REVERT: I 155 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.8082 (mmm160) REVERT: I 360 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6343 (tp30) REVERT: I 364 GLU cc_start: 0.8510 (tt0) cc_final: 0.8116 (mp0) REVERT: I 446 GLU cc_start: 0.8334 (tt0) cc_final: 0.8051 (tm-30) REVERT: J 10 LYS cc_start: 0.8512 (mttt) cc_final: 0.7923 (mmtm) REVERT: J 11 ASP cc_start: 0.8019 (m-30) cc_final: 0.7598 (t0) REVERT: J 170 ASP cc_start: 0.7466 (t70) cc_final: 0.7018 (t0) REVERT: J 255 ARG cc_start: 0.3552 (tpp80) cc_final: 0.2560 (ttm170) REVERT: J 340 ILE cc_start: 0.6077 (mt) cc_final: 0.5814 (tt) REVERT: J 446 GLU cc_start: 0.7634 (tt0) cc_final: 0.7350 (tp30) REVERT: K 10 LYS cc_start: 0.8200 (mttt) cc_final: 0.7611 (tppt) REVERT: K 44 VAL cc_start: 0.8970 (m) cc_final: 0.8686 (t) REVERT: K 119 GLU cc_start: 0.8545 (tp30) cc_final: 0.8183 (tm-30) REVERT: K 140 TYR cc_start: 0.6829 (t80) cc_final: 0.6480 (t80) REVERT: K 155 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7746 (tpm170) REVERT: K 175 GLU cc_start: 0.5678 (mp0) cc_final: 0.5045 (pt0) REVERT: K 178 ASN cc_start: 0.6463 (m110) cc_final: 0.5948 (t0) REVERT: K 305 MET cc_start: 0.7649 (mtt) cc_final: 0.7341 (mtt) REVERT: K 338 ARG cc_start: 0.6693 (ptt-90) cc_final: 0.6307 (pmt-80) REVERT: K 340 ILE cc_start: 0.7767 (mt) cc_final: 0.7145 (mp) REVERT: K 496 ASP cc_start: 0.8688 (t70) cc_final: 0.8174 (m-30) REVERT: K 504 MET cc_start: 0.7433 (ttm) cc_final: 0.6991 (ttm) REVERT: L 11 ASP cc_start: 0.8091 (m-30) cc_final: 0.7869 (t0) REVERT: L 116 ASP cc_start: 0.8420 (t0) cc_final: 0.7971 (m-30) REVERT: L 145 THR cc_start: 0.8603 (m) cc_final: 0.8360 (p) REVERT: L 285 PRO cc_start: 0.4507 (Cg_exo) cc_final: 0.4192 (Cg_endo) REVERT: L 442 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7972 (ttpp) REVERT: L 446 GLU cc_start: 0.7565 (tt0) cc_final: 0.7233 (pp20) REVERT: L 476 LYS cc_start: 0.8746 (tttt) cc_final: 0.8346 (ttmt) REVERT: M 10 LYS cc_start: 0.8673 (mttt) cc_final: 0.8293 (pttm) REVERT: M 38 VAL cc_start: 0.9242 (t) cc_final: 0.8962 (p) REVERT: M 116 ASP cc_start: 0.8500 (t0) cc_final: 0.8245 (m-30) REVERT: M 191 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6816 (mp) REVERT: M 340 ILE cc_start: 0.6627 (mt) cc_final: 0.6128 (tt) REVERT: N 299 LEU cc_start: 0.5165 (mt) cc_final: 0.4759 (mp) REVERT: N 334 LEU cc_start: 0.7009 (mt) cc_final: 0.6577 (tp) REVERT: N 488 ASN cc_start: 0.6493 (p0) cc_final: 0.6137 (p0) outliers start: 64 outliers final: 16 residues processed: 1084 average time/residue: 0.5758 time to fit residues: 1031.7575 Evaluate side-chains 521 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 502 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain G residue 463 ILE Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain N residue 463 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 4.9990 chunk 573 optimal weight: 9.9990 chunk 317 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 386 optimal weight: 2.9990 chunk 306 optimal weight: 0.5980 chunk 592 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 chunk 441 optimal weight: 0.9980 chunk 686 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 185 GLN B 109 GLN C 36 GLN C 109 GLN D 109 GLN E 109 GLN E 242 HIS E 267 GLN E 355 HIS F 109 GLN F 355 HIS G 109 GLN G 164 ASN H 109 GLN H 185 GLN I 109 GLN J 36 GLN J 109 GLN ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 GLN L 109 GLN L 242 HIS L 267 GLN L 355 HIS M 109 GLN N 109 GLN N 164 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 59022 Z= 0.188 Angle : 0.515 8.207 80066 Z= 0.279 Chirality : 0.039 0.180 9452 Planarity : 0.004 0.054 10410 Dihedral : 4.629 59.205 8188 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.54 % Allowed : 9.21 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.09), residues: 7560 helix: 0.69 (0.08), residues: 3964 sheet: -2.06 (0.14), residues: 1022 loop : -1.38 (0.11), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 282 HIS 0.006 0.001 HIS J 355 PHE 0.018 0.001 PHE K 214 TYR 0.024 0.001 TYR B 140 ARG 0.004 0.000 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 592 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8306 (tp30) cc_final: 0.8086 (mm-30) REVERT: A 418 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7861 (ttm-80) REVERT: A 487 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8420 (pm20) REVERT: A 495 ASP cc_start: 0.8898 (t0) cc_final: 0.8579 (m-30) REVERT: A 508 THR cc_start: 0.7426 (m) cc_final: 0.7161 (p) REVERT: B 64 GLU cc_start: 0.8305 (tp30) cc_final: 0.7742 (tt0) REVERT: B 116 ASP cc_start: 0.8168 (t0) cc_final: 0.7844 (m-30) REVERT: B 140 TYR cc_start: 0.8301 (t80) cc_final: 0.8043 (t80) REVERT: B 155 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7959 (mmm160) REVERT: B 282 TRP cc_start: 0.5126 (p-90) cc_final: 0.4840 (p-90) REVERT: B 370 ASP cc_start: 0.7925 (m-30) cc_final: 0.7405 (p0) REVERT: B 425 ILE cc_start: 0.8570 (mt) cc_final: 0.8201 (tt) REVERT: B 446 GLU cc_start: 0.8212 (tt0) cc_final: 0.7905 (tm-30) REVERT: C 170 ASP cc_start: 0.7315 (t70) cc_final: 0.7088 (t0) REVERT: C 405 GLU cc_start: 0.7542 (tp30) cc_final: 0.7243 (tp30) REVERT: C 446 GLU cc_start: 0.7334 (tt0) cc_final: 0.7036 (tp30) REVERT: D 44 VAL cc_start: 0.8882 (m) cc_final: 0.8562 (t) REVERT: D 75 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: D 119 GLU cc_start: 0.8129 (tp30) cc_final: 0.7835 (tm-30) REVERT: D 140 TYR cc_start: 0.6898 (t80) cc_final: 0.6562 (t80) REVERT: D 155 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7590 (tpm170) REVERT: D 178 ASN cc_start: 0.6374 (m110) cc_final: 0.5874 (t0) REVERT: D 305 MET cc_start: 0.7267 (mtt) cc_final: 0.6979 (mtt) REVERT: D 333 GLU cc_start: 0.6930 (tt0) cc_final: 0.6568 (tm-30) REVERT: D 338 ARG cc_start: 0.6436 (ptt-90) cc_final: 0.6060 (pmt-80) REVERT: D 504 MET cc_start: 0.7464 (ttm) cc_final: 0.7230 (ttm) REVERT: E 144 LEU cc_start: 0.8436 (tp) cc_final: 0.8196 (tp) REVERT: E 145 THR cc_start: 0.8420 (m) cc_final: 0.8085 (p) REVERT: E 476 LYS cc_start: 0.8902 (tttt) cc_final: 0.8617 (ttmm) REVERT: F 38 VAL cc_start: 0.9073 (t) cc_final: 0.8834 (p) REVERT: F 116 ASP cc_start: 0.8375 (t0) cc_final: 0.7887 (m-30) REVERT: F 119 GLU cc_start: 0.8381 (tp30) cc_final: 0.7961 (tm-30) REVERT: F 334 LEU cc_start: 0.5726 (tp) cc_final: 0.5471 (tp) REVERT: F 410 TYR cc_start: 0.6427 (m-80) cc_final: 0.6185 (m-80) REVERT: F 469 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8010 (ttp-110) REVERT: F 499 ASN cc_start: 0.8268 (m-40) cc_final: 0.7852 (t0) REVERT: G 144 LEU cc_start: 0.8460 (pp) cc_final: 0.7658 (tp) REVERT: G 168 TYR cc_start: 0.6995 (m-80) cc_final: 0.6779 (m-80) REVERT: G 191 ILE cc_start: 0.7011 (pt) cc_final: 0.6699 (pt) REVERT: G 193 MET cc_start: 0.5160 (tmm) cc_final: 0.4345 (mtt) REVERT: G 210 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6740 (tp30) REVERT: G 266 MET cc_start: 0.3199 (OUTLIER) cc_final: 0.2729 (ttp) REVERT: G 418 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7864 (tpp-160) REVERT: H 119 GLU cc_start: 0.8331 (tp30) cc_final: 0.8131 (mm-30) REVERT: H 487 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8372 (pm20) REVERT: H 495 ASP cc_start: 0.8893 (t0) cc_final: 0.8586 (m-30) REVERT: H 508 THR cc_start: 0.7531 (m) cc_final: 0.7257 (p) REVERT: I 64 GLU cc_start: 0.8296 (tp30) cc_final: 0.7735 (tt0) REVERT: I 116 ASP cc_start: 0.8151 (t0) cc_final: 0.7836 (m-30) REVERT: I 140 TYR cc_start: 0.8300 (t80) cc_final: 0.8023 (t80) REVERT: I 155 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7979 (mmm160) REVERT: I 282 TRP cc_start: 0.5153 (p-90) cc_final: 0.4872 (p-90) REVERT: I 370 ASP cc_start: 0.7889 (m-30) cc_final: 0.7353 (p0) REVERT: I 425 ILE cc_start: 0.8569 (mt) cc_final: 0.8210 (tt) REVERT: I 446 GLU cc_start: 0.8215 (tt0) cc_final: 0.7905 (tm-30) REVERT: J 170 ASP cc_start: 0.7332 (t70) cc_final: 0.7099 (t0) REVERT: J 255 ARG cc_start: 0.3219 (tpp80) cc_final: 0.3009 (ttm170) REVERT: J 299 LEU cc_start: 0.5628 (mt) cc_final: 0.5393 (tp) REVERT: J 446 GLU cc_start: 0.7337 (tt0) cc_final: 0.7042 (tp30) REVERT: K 44 VAL cc_start: 0.8882 (m) cc_final: 0.8596 (t) REVERT: K 75 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: K 119 GLU cc_start: 0.8088 (tp30) cc_final: 0.7821 (tm-30) REVERT: K 140 TYR cc_start: 0.6836 (t80) cc_final: 0.6503 (t80) REVERT: K 155 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7598 (tpm170) REVERT: K 178 ASN cc_start: 0.6405 (m110) cc_final: 0.5910 (t0) REVERT: K 305 MET cc_start: 0.7291 (mtt) cc_final: 0.7006 (mtt) REVERT: K 333 GLU cc_start: 0.6948 (tt0) cc_final: 0.6547 (tm-30) REVERT: K 338 ARG cc_start: 0.6428 (ptt-90) cc_final: 0.6091 (pmt-80) REVERT: K 504 MET cc_start: 0.7485 (ttm) cc_final: 0.7254 (ttm) REVERT: L 145 THR cc_start: 0.8416 (m) cc_final: 0.8061 (p) REVERT: L 476 LYS cc_start: 0.8892 (tttt) cc_final: 0.8601 (ttmm) REVERT: L 487 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7902 (pm20) REVERT: M 38 VAL cc_start: 0.9051 (t) cc_final: 0.8799 (p) REVERT: M 116 ASP cc_start: 0.8359 (t0) cc_final: 0.7876 (m-30) REVERT: M 334 LEU cc_start: 0.5741 (tp) cc_final: 0.5484 (tp) REVERT: M 410 TYR cc_start: 0.6257 (m-80) cc_final: 0.6027 (m-80) REVERT: M 499 ASN cc_start: 0.8279 (m-40) cc_final: 0.7847 (t0) REVERT: N 47 LYS cc_start: 0.8452 (tttt) cc_final: 0.8128 (ttpt) REVERT: N 144 LEU cc_start: 0.8427 (pp) cc_final: 0.7618 (tp) REVERT: N 168 TYR cc_start: 0.7006 (m-80) cc_final: 0.6783 (m-80) REVERT: N 193 MET cc_start: 0.5161 (tmm) cc_final: 0.4558 (mtt) REVERT: N 266 MET cc_start: 0.3215 (OUTLIER) cc_final: 0.2737 (ttp) REVERT: N 316 ASP cc_start: 0.5567 (m-30) cc_final: 0.5350 (t0) outliers start: 95 outliers final: 53 residues processed: 666 average time/residue: 0.5241 time to fit residues: 594.4752 Evaluate side-chains 493 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 436 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 417 ILE Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 440 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 266 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 571 optimal weight: 7.9990 chunk 467 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 687 optimal weight: 6.9990 chunk 742 optimal weight: 9.9990 chunk 612 optimal weight: 10.0000 chunk 682 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN F 18 GLN F 328 GLN G 164 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 HIS ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 328 GLN M 355 HIS N 164 ASN ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59022 Z= 0.203 Angle : 0.484 8.600 80066 Z= 0.256 Chirality : 0.039 0.143 9452 Planarity : 0.004 0.050 10410 Dihedral : 4.370 59.745 8178 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.35 % Allowed : 10.62 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 7560 helix: 1.58 (0.08), residues: 3980 sheet: -1.58 (0.15), residues: 998 loop : -1.04 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 282 HIS 0.004 0.001 HIS F 475 PHE 0.011 0.001 PHE C 217 TYR 0.020 0.002 TYR K 378 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 478 time to evaluate : 4.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8323 (tp30) cc_final: 0.8080 (mm-30) REVERT: A 418 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7798 (ttm-80) REVERT: A 487 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8420 (pm20) REVERT: A 495 ASP cc_start: 0.8871 (t0) cc_final: 0.8572 (m-30) REVERT: A 508 THR cc_start: 0.7439 (m) cc_final: 0.7171 (p) REVERT: B 64 GLU cc_start: 0.8464 (tp30) cc_final: 0.7799 (tt0) REVERT: B 93 MET cc_start: 0.8313 (ttp) cc_final: 0.8106 (ttp) REVERT: B 116 ASP cc_start: 0.8118 (t0) cc_final: 0.7812 (m-30) REVERT: B 155 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7974 (mmm160) REVERT: B 282 TRP cc_start: 0.5184 (p-90) cc_final: 0.4983 (p-90) REVERT: B 370 ASP cc_start: 0.7934 (m-30) cc_final: 0.7364 (p0) REVERT: B 425 ILE cc_start: 0.8519 (mt) cc_final: 0.8138 (tt) REVERT: B 446 GLU cc_start: 0.8164 (tt0) cc_final: 0.7823 (tm-30) REVERT: C 11 ASP cc_start: 0.7819 (m-30) cc_final: 0.7344 (t0) REVERT: C 170 ASP cc_start: 0.7230 (t70) cc_final: 0.6920 (t0) REVERT: C 175 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 446 GLU cc_start: 0.7404 (tt0) cc_final: 0.7124 (tp30) REVERT: D 44 VAL cc_start: 0.8763 (m) cc_final: 0.8503 (t) REVERT: D 75 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: D 119 GLU cc_start: 0.8193 (tp30) cc_final: 0.7864 (tm-30) REVERT: D 140 TYR cc_start: 0.6722 (t80) cc_final: 0.6231 (t80) REVERT: D 178 ASN cc_start: 0.6389 (m110) cc_final: 0.5857 (t0) REVERT: D 338 ARG cc_start: 0.6323 (ptt-90) cc_final: 0.6111 (pmt-80) REVERT: D 446 GLU cc_start: 0.7826 (tt0) cc_final: 0.7114 (mm-30) REVERT: D 504 MET cc_start: 0.7573 (ttm) cc_final: 0.7223 (ttm) REVERT: E 145 THR cc_start: 0.8441 (m) cc_final: 0.8095 (p) REVERT: E 160 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7927 (tt) REVERT: E 285 PRO cc_start: 0.5149 (Cg_exo) cc_final: 0.4914 (Cg_endo) REVERT: E 349 GLU cc_start: 0.5976 (mt-10) cc_final: 0.5451 (tp30) REVERT: E 476 LYS cc_start: 0.8883 (tttt) cc_final: 0.8598 (ttmm) REVERT: F 10 LYS cc_start: 0.8330 (mttt) cc_final: 0.7916 (pttm) REVERT: F 38 VAL cc_start: 0.9145 (t) cc_final: 0.8843 (p) REVERT: F 116 ASP cc_start: 0.8336 (t0) cc_final: 0.7936 (m-30) REVERT: F 119 GLU cc_start: 0.8351 (tp30) cc_final: 0.7922 (tm-30) REVERT: F 390 LEU cc_start: 0.6095 (mt) cc_final: 0.5830 (mt) REVERT: F 410 TYR cc_start: 0.6399 (m-80) cc_final: 0.6076 (m-80) REVERT: F 499 ASN cc_start: 0.8332 (m-40) cc_final: 0.7868 (t0) REVERT: G 144 LEU cc_start: 0.8544 (pp) cc_final: 0.7862 (tp) REVERT: G 168 TYR cc_start: 0.7186 (m-80) cc_final: 0.6951 (m-80) REVERT: G 210 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6589 (tp30) REVERT: G 266 MET cc_start: 0.3197 (OUTLIER) cc_final: 0.2794 (ttm) REVERT: G 418 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7739 (tpp-160) REVERT: G 446 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7242 (mm-30) REVERT: H 487 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8407 (pm20) REVERT: H 495 ASP cc_start: 0.8868 (t0) cc_final: 0.8577 (m-30) REVERT: H 508 THR cc_start: 0.7397 (m) cc_final: 0.7120 (p) REVERT: I 64 GLU cc_start: 0.8453 (tp30) cc_final: 0.7784 (tt0) REVERT: I 93 MET cc_start: 0.8311 (ttp) cc_final: 0.8106 (ttp) REVERT: I 116 ASP cc_start: 0.8115 (t0) cc_final: 0.7808 (m-30) REVERT: I 370 ASP cc_start: 0.7927 (m-30) cc_final: 0.7353 (p0) REVERT: I 446 GLU cc_start: 0.8166 (tt0) cc_final: 0.7818 (tm-30) REVERT: J 11 ASP cc_start: 0.7817 (m-30) cc_final: 0.7344 (t0) REVERT: J 170 ASP cc_start: 0.7246 (t70) cc_final: 0.6927 (t0) REVERT: J 175 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7084 (mt-10) REVERT: J 446 GLU cc_start: 0.7406 (tt0) cc_final: 0.7137 (tp30) REVERT: K 44 VAL cc_start: 0.8775 (m) cc_final: 0.8531 (t) REVERT: K 119 GLU cc_start: 0.8147 (tp30) cc_final: 0.7821 (tm-30) REVERT: K 140 TYR cc_start: 0.6721 (t80) cc_final: 0.6237 (t80) REVERT: K 178 ASN cc_start: 0.6358 (m110) cc_final: 0.5826 (t0) REVERT: K 305 MET cc_start: 0.7382 (mtt) cc_final: 0.7150 (mtt) REVERT: K 333 GLU cc_start: 0.6955 (tt0) cc_final: 0.6557 (tm-30) REVERT: K 338 ARG cc_start: 0.6362 (ptt-90) cc_final: 0.6092 (pmt-80) REVERT: K 446 GLU cc_start: 0.7844 (tt0) cc_final: 0.7141 (mm-30) REVERT: K 504 MET cc_start: 0.7576 (ttm) cc_final: 0.7220 (ttm) REVERT: L 145 THR cc_start: 0.8308 (m) cc_final: 0.7948 (p) REVERT: L 285 PRO cc_start: 0.5151 (Cg_exo) cc_final: 0.4949 (Cg_endo) REVERT: L 476 LYS cc_start: 0.8876 (tttt) cc_final: 0.8589 (ttmm) REVERT: M 10 LYS cc_start: 0.8325 (mttt) cc_final: 0.7905 (pttm) REVERT: M 38 VAL cc_start: 0.9137 (t) cc_final: 0.8827 (p) REVERT: M 116 ASP cc_start: 0.8341 (t0) cc_final: 0.7947 (m-30) REVERT: M 148 ASN cc_start: 0.3706 (OUTLIER) cc_final: 0.3432 (m-40) REVERT: M 149 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7600 (mp10) REVERT: M 410 TYR cc_start: 0.6537 (m-80) cc_final: 0.6233 (m-80) REVERT: M 499 ASN cc_start: 0.8297 (m-40) cc_final: 0.7845 (t0) REVERT: N 193 MET cc_start: 0.5476 (tmm) cc_final: 0.4813 (mtt) REVERT: N 266 MET cc_start: 0.3216 (OUTLIER) cc_final: 0.2805 (ttm) REVERT: N 446 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7139 (mm-30) outliers start: 145 outliers final: 78 residues processed: 597 average time/residue: 0.5040 time to fit residues: 524.8014 Evaluate side-chains 501 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 418 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 386 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 545 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 395 VAL Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 417 ILE Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 440 THR Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 148 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 10.0000 chunk 517 optimal weight: 5.9990 chunk 356 optimal weight: 0.0000 chunk 76 optimal weight: 9.9990 chunk 328 optimal weight: 0.0970 chunk 461 optimal weight: 10.0000 chunk 690 optimal weight: 1.9990 chunk 730 optimal weight: 30.0000 chunk 360 optimal weight: 20.0000 chunk 654 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN B 262 ASN B 328 GLN ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 HIS G 262 ASN G 307 ASN G 328 GLN H 355 HIS I 262 ASN I 328 GLN ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 HIS M 272 HIS M 465 ASN N 307 ASN N 328 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59022 Z= 0.188 Angle : 0.459 10.484 80066 Z= 0.241 Chirality : 0.038 0.153 9452 Planarity : 0.003 0.047 10410 Dihedral : 4.271 59.420 8178 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 12.26 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7560 helix: 1.85 (0.08), residues: 3976 sheet: -1.32 (0.15), residues: 1030 loop : -0.88 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 282 HIS 0.003 0.001 HIS N 100 PHE 0.011 0.001 PHE J 217 TYR 0.024 0.001 TYR B 140 ARG 0.003 0.000 ARG M 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 463 time to evaluate : 4.831 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: A 418 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7857 (ttm-80) REVERT: A 487 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 495 ASP cc_start: 0.8925 (t0) cc_final: 0.8627 (m-30) REVERT: A 508 THR cc_start: 0.7434 (m) cc_final: 0.7150 (p) REVERT: B 64 GLU cc_start: 0.8466 (tp30) cc_final: 0.7834 (tt0) REVERT: B 116 ASP cc_start: 0.8099 (t0) cc_final: 0.7792 (m-30) REVERT: B 155 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7868 (mmm160) REVERT: B 370 ASP cc_start: 0.7934 (m-30) cc_final: 0.7372 (p0) REVERT: B 386 LEU cc_start: 0.8169 (tp) cc_final: 0.7943 (mp) REVERT: B 446 GLU cc_start: 0.8139 (tt0) cc_final: 0.7808 (tm-30) REVERT: C 11 ASP cc_start: 0.7701 (m-30) cc_final: 0.7221 (t0) REVERT: C 75 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: C 170 ASP cc_start: 0.7199 (t70) cc_final: 0.6886 (t0) REVERT: C 175 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7070 (mt-10) REVERT: C 446 GLU cc_start: 0.7411 (tt0) cc_final: 0.7131 (tp30) REVERT: D 44 VAL cc_start: 0.8810 (m) cc_final: 0.8544 (t) REVERT: D 75 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: D 140 TYR cc_start: 0.6678 (t80) cc_final: 0.6148 (t80) REVERT: D 178 ASN cc_start: 0.6395 (m110) cc_final: 0.5834 (t0) REVERT: D 338 ARG cc_start: 0.6295 (ptt-90) cc_final: 0.6090 (pmt-80) REVERT: D 417 ILE cc_start: 0.8701 (mt) cc_final: 0.8431 (tt) REVERT: D 446 GLU cc_start: 0.7740 (tt0) cc_final: 0.7039 (mm-30) REVERT: D 504 MET cc_start: 0.7560 (ttm) cc_final: 0.7218 (ttm) REVERT: D 519 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7792 (pt) REVERT: E 119 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8180 (mp0) REVERT: E 145 THR cc_start: 0.8417 (m) cc_final: 0.8061 (p) REVERT: E 183 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7754 (mm) REVERT: E 476 LYS cc_start: 0.8925 (tttt) cc_final: 0.8645 (ttmm) REVERT: F 10 LYS cc_start: 0.8302 (mttt) cc_final: 0.7866 (pttm) REVERT: F 116 ASP cc_start: 0.8281 (t0) cc_final: 0.7918 (m-30) REVERT: F 119 GLU cc_start: 0.8377 (tp30) cc_final: 0.7952 (tm-30) REVERT: G 168 TYR cc_start: 0.7260 (m-80) cc_final: 0.7017 (m-80) REVERT: G 210 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6518 (tp30) REVERT: G 266 MET cc_start: 0.3191 (OUTLIER) cc_final: 0.2828 (mmt) REVERT: G 298 GLU cc_start: 0.5983 (pt0) cc_final: 0.5190 (tt0) REVERT: G 442 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7608 (tttp) REVERT: G 446 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7184 (mm-30) REVERT: H 487 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8219 (mp0) REVERT: H 495 ASP cc_start: 0.8926 (t0) cc_final: 0.8644 (m-30) REVERT: H 508 THR cc_start: 0.7451 (m) cc_final: 0.7179 (p) REVERT: I 64 GLU cc_start: 0.8460 (tp30) cc_final: 0.7830 (tt0) REVERT: I 116 ASP cc_start: 0.8115 (t0) cc_final: 0.7814 (m-30) REVERT: I 370 ASP cc_start: 0.7926 (m-30) cc_final: 0.7338 (p0) REVERT: I 386 LEU cc_start: 0.8170 (tp) cc_final: 0.7950 (mp) REVERT: I 446 GLU cc_start: 0.8115 (tt0) cc_final: 0.7812 (tm-30) REVERT: J 11 ASP cc_start: 0.7694 (m-30) cc_final: 0.7220 (t0) REVERT: J 170 ASP cc_start: 0.7200 (t70) cc_final: 0.6876 (t0) REVERT: J 175 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7081 (mt-10) REVERT: J 446 GLU cc_start: 0.7418 (tt0) cc_final: 0.7137 (tp30) REVERT: K 44 VAL cc_start: 0.8814 (m) cc_final: 0.8558 (t) REVERT: K 140 TYR cc_start: 0.6681 (t80) cc_final: 0.6372 (t80) REVERT: K 178 ASN cc_start: 0.6459 (m110) cc_final: 0.5898 (t0) REVERT: K 333 GLU cc_start: 0.6909 (tt0) cc_final: 0.6552 (tm-30) REVERT: K 338 ARG cc_start: 0.6377 (ptt-90) cc_final: 0.6171 (pmt-80) REVERT: K 417 ILE cc_start: 0.8706 (mt) cc_final: 0.8438 (tt) REVERT: K 446 GLU cc_start: 0.7740 (tt0) cc_final: 0.7074 (mm-30) REVERT: K 504 MET cc_start: 0.7604 (ttm) cc_final: 0.7254 (ttm) REVERT: K 519 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7794 (pt) REVERT: L 119 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8155 (mp0) REVERT: L 145 THR cc_start: 0.8403 (m) cc_final: 0.8067 (p) REVERT: L 476 LYS cc_start: 0.8916 (tttt) cc_final: 0.8635 (ttmm) REVERT: M 10 LYS cc_start: 0.8280 (mttt) cc_final: 0.7847 (pttm) REVERT: M 116 ASP cc_start: 0.8292 (t0) cc_final: 0.7917 (m-30) REVERT: M 149 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7626 (mp10) REVERT: M 499 ASN cc_start: 0.8335 (m-40) cc_final: 0.7873 (t0) REVERT: N 144 LEU cc_start: 0.8398 (pp) cc_final: 0.7567 (tp) REVERT: N 266 MET cc_start: 0.3217 (OUTLIER) cc_final: 0.2847 (mmt) REVERT: N 298 GLU cc_start: 0.6053 (pt0) cc_final: 0.5269 (tt0) REVERT: N 442 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7487 (tttp) REVERT: N 446 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7197 (mm-30) outliers start: 129 outliers final: 95 residues processed: 574 average time/residue: 0.5355 time to fit residues: 530.4718 Evaluate side-chains 519 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 417 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 421 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 294 ILE Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 128 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 545 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 135 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 395 VAL Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 440 THR Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 419 SER Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 425 ILE Chi-restraints excluded: chain N residue 432 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 20.0000 chunk 414 optimal weight: 40.0000 chunk 10 optimal weight: 4.9990 chunk 544 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 623 optimal weight: 6.9990 chunk 505 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 655 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 182 GLN A 355 HIS B 66 HIS B 328 GLN ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 379 ASN F 148 ASN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS G 423 ASN G 465 ASN H 182 GLN I 66 HIS ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN J 355 HIS K 460 ASN L 262 ASN L 379 ASN N 262 ASN ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS N 423 ASN N 465 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 59022 Z= 0.643 Angle : 0.780 18.186 80066 Z= 0.405 Chirality : 0.050 0.191 9452 Planarity : 0.006 0.052 10410 Dihedral : 5.564 56.976 8178 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.23 % Allowed : 12.71 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 7560 helix: 0.56 (0.08), residues: 4004 sheet: -0.97 (0.16), residues: 948 loop : -1.27 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 199 HIS 0.010 0.002 HIS F 475 PHE 0.029 0.003 PHE L 438 TYR 0.030 0.003 TYR B 140 ARG 0.008 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 452 time to evaluate : 4.937 Fit side-chains revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8442 (m-30) cc_final: 0.8219 (m-30) REVERT: A 182 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: A 344 THR cc_start: 0.5577 (OUTLIER) cc_final: 0.5336 (m) REVERT: A 418 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7807 (ttm-80) REVERT: B 64 GLU cc_start: 0.8816 (tp30) cc_final: 0.8109 (tt0) REVERT: B 446 GLU cc_start: 0.8074 (tt0) cc_final: 0.7626 (tm-30) REVERT: B 499 ASN cc_start: 0.8632 (m-40) cc_final: 0.8084 (t0) REVERT: C 10 LYS cc_start: 0.8461 (mttt) cc_final: 0.7792 (mmtt) REVERT: C 11 ASP cc_start: 0.7899 (m-30) cc_final: 0.7538 (t0) REVERT: C 170 ASP cc_start: 0.6799 (t70) cc_final: 0.6575 (t0) REVERT: C 222 ARG cc_start: 0.2765 (mtt180) cc_final: 0.2419 (mtt-85) REVERT: C 421 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (mp) REVERT: C 511 ILE cc_start: 0.8487 (mt) cc_final: 0.8221 (pt) REVERT: D 64 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8295 (tp30) REVERT: D 140 TYR cc_start: 0.7102 (t80) cc_final: 0.6836 (t80) REVERT: D 178 ASN cc_start: 0.6681 (m110) cc_final: 0.6151 (t0) REVERT: D 338 ARG cc_start: 0.6294 (ptt-90) cc_final: 0.5998 (pmt-80) REVERT: D 370 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6390 (t0) REVERT: E 145 THR cc_start: 0.8446 (m) cc_final: 0.8079 (p) REVERT: E 404 LYS cc_start: 0.6907 (ptpp) cc_final: 0.6629 (tmtt) REVERT: E 476 LYS cc_start: 0.8960 (tttt) cc_final: 0.8601 (ttmm) REVERT: F 10 LYS cc_start: 0.8367 (mttt) cc_final: 0.7896 (pttm) REVERT: F 116 ASP cc_start: 0.8449 (t0) cc_final: 0.8113 (m-30) REVERT: F 119 GLU cc_start: 0.8558 (tp30) cc_final: 0.7948 (tm-30) REVERT: G 10 LYS cc_start: 0.8717 (mttt) cc_final: 0.8120 (mmmt) REVERT: G 210 GLU cc_start: 0.6153 (mt-10) cc_final: 0.5947 (tp30) REVERT: G 266 MET cc_start: 0.2486 (OUTLIER) cc_final: 0.2023 (mmt) REVERT: G 446 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7550 (mm-30) REVERT: H 11 ASP cc_start: 0.8373 (m-30) cc_final: 0.8133 (m-30) REVERT: H 182 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: I 64 GLU cc_start: 0.8821 (tp30) cc_final: 0.8108 (tt0) REVERT: I 446 GLU cc_start: 0.8096 (tt0) cc_final: 0.7665 (tm-30) REVERT: I 499 ASN cc_start: 0.8645 (m-40) cc_final: 0.8102 (t0) REVERT: J 10 LYS cc_start: 0.8453 (mttt) cc_final: 0.7787 (mmtt) REVERT: J 11 ASP cc_start: 0.7896 (m-30) cc_final: 0.7537 (t0) REVERT: J 170 ASP cc_start: 0.6801 (t70) cc_final: 0.6575 (t0) REVERT: J 421 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8478 (mp) REVERT: J 511 ILE cc_start: 0.8477 (mt) cc_final: 0.8203 (pt) REVERT: K 140 TYR cc_start: 0.7114 (t80) cc_final: 0.6853 (t80) REVERT: K 178 ASN cc_start: 0.6526 (m110) cc_final: 0.6036 (t0) REVERT: K 338 ARG cc_start: 0.6414 (ptt-90) cc_final: 0.6172 (pmt-80) REVERT: K 370 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6462 (t0) REVERT: K 446 GLU cc_start: 0.7990 (tt0) cc_final: 0.7397 (mm-30) REVERT: K 504 MET cc_start: 0.8057 (ttm) cc_final: 0.7664 (ttm) REVERT: L 145 THR cc_start: 0.8395 (m) cc_final: 0.8035 (p) REVERT: L 404 LYS cc_start: 0.6943 (ptpp) cc_final: 0.6662 (tmtt) REVERT: L 476 LYS cc_start: 0.8972 (tttt) cc_final: 0.8617 (ttmm) REVERT: M 10 LYS cc_start: 0.8358 (mttt) cc_final: 0.7886 (pttm) REVERT: M 116 ASP cc_start: 0.8433 (t0) cc_final: 0.8097 (m-30) REVERT: M 149 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7593 (mp10) REVERT: N 10 LYS cc_start: 0.8771 (mttt) cc_final: 0.8166 (mmmt) REVERT: N 266 MET cc_start: 0.2500 (OUTLIER) cc_final: 0.2041 (mmt) REVERT: N 446 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7519 (mm-30) outliers start: 199 outliers final: 113 residues processed: 623 average time/residue: 0.5031 time to fit residues: 547.0621 Evaluate side-chains 504 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 382 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 488 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 481 ASP Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 294 ILE Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 542 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 395 VAL Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 488 ASN Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 545 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 135 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 370 ASP Chi-restraints excluded: chain K residue 417 ILE Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 440 THR Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain M residue 481 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 522 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Chi-restraints excluded: chain N residue 545 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 7.9990 chunk 658 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 429 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 731 optimal weight: 20.0000 chunk 607 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 384 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN E 328 GLN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 ASN ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 GLN L 331 GLN M 499 ASN ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 59022 Z= 0.377 Angle : 0.593 16.643 80066 Z= 0.305 Chirality : 0.042 0.172 9452 Planarity : 0.004 0.050 10410 Dihedral : 4.841 59.313 8172 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.68 % Allowed : 14.35 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7560 helix: 0.92 (0.08), residues: 4000 sheet: -0.80 (0.18), residues: 850 loop : -1.25 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 199 HIS 0.007 0.001 HIS M 475 PHE 0.015 0.002 PHE J 491 TYR 0.025 0.002 TYR B 140 ARG 0.006 0.000 ARG I 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 406 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: A 344 THR cc_start: 0.5126 (OUTLIER) cc_final: 0.4849 (m) REVERT: A 418 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7936 (ttm-80) REVERT: A 487 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8433 (mp0) REVERT: B 64 GLU cc_start: 0.8751 (tp30) cc_final: 0.8048 (tt0) REVERT: B 116 ASP cc_start: 0.8228 (t0) cc_final: 0.7889 (m-30) REVERT: B 236 ASN cc_start: 0.3330 (m110) cc_final: 0.3016 (t0) REVERT: B 262 ASN cc_start: 0.1341 (m110) cc_final: 0.1117 (m-40) REVERT: B 446 GLU cc_start: 0.8145 (tt0) cc_final: 0.7708 (tm-30) REVERT: B 499 ASN cc_start: 0.8599 (m-40) cc_final: 0.8058 (t0) REVERT: C 11 ASP cc_start: 0.7918 (m-30) cc_final: 0.7431 (t0) REVERT: C 172 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6638 (mp0) REVERT: C 222 ARG cc_start: 0.2719 (mtt180) cc_final: 0.2419 (mtt-85) REVERT: C 398 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5862 (mm-30) REVERT: C 511 ILE cc_start: 0.8496 (mt) cc_final: 0.8121 (pt) REVERT: D 140 TYR cc_start: 0.7233 (t80) cc_final: 0.6867 (t80) REVERT: D 178 ASN cc_start: 0.6710 (m110) cc_final: 0.6278 (t0) REVERT: D 310 MET cc_start: 0.3902 (mmp) cc_final: 0.3337 (mtp) REVERT: D 338 ARG cc_start: 0.6393 (ptt-90) cc_final: 0.6185 (pmt-80) REVERT: D 411 GLU cc_start: 0.6584 (pt0) cc_final: 0.6195 (mt-10) REVERT: D 417 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8399 (tt) REVERT: D 504 MET cc_start: 0.7821 (ttm) cc_final: 0.7442 (ttm) REVERT: E 119 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8263 (mp0) REVERT: E 145 THR cc_start: 0.8417 (m) cc_final: 0.8038 (p) REVERT: E 404 LYS cc_start: 0.6815 (ptpp) cc_final: 0.6509 (tmtt) REVERT: E 476 LYS cc_start: 0.8964 (tttt) cc_final: 0.8611 (ttmm) REVERT: F 10 LYS cc_start: 0.8331 (mttt) cc_final: 0.7839 (pttm) REVERT: F 78 THR cc_start: 0.6874 (OUTLIER) cc_final: 0.6467 (p) REVERT: F 116 ASP cc_start: 0.8335 (t0) cc_final: 0.8026 (m-30) REVERT: F 119 GLU cc_start: 0.8504 (tp30) cc_final: 0.7759 (tp30) REVERT: G 193 MET cc_start: 0.5431 (tmm) cc_final: 0.4989 (tpp) REVERT: G 266 MET cc_start: 0.2536 (OUTLIER) cc_final: 0.2084 (mmt) REVERT: G 442 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7711 (tttp) REVERT: H 182 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: H 252 LEU cc_start: 0.6191 (mt) cc_final: 0.5972 (pp) REVERT: H 487 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8427 (mp0) REVERT: I 64 GLU cc_start: 0.8755 (tp30) cc_final: 0.8054 (tt0) REVERT: I 116 ASP cc_start: 0.8226 (t0) cc_final: 0.7887 (m-30) REVERT: I 236 ASN cc_start: 0.3456 (m110) cc_final: 0.3150 (t0) REVERT: I 262 ASN cc_start: 0.1344 (m110) cc_final: 0.1118 (m-40) REVERT: I 446 GLU cc_start: 0.8162 (tt0) cc_final: 0.7743 (tm-30) REVERT: I 499 ASN cc_start: 0.8596 (m-40) cc_final: 0.8056 (t0) REVERT: J 11 ASP cc_start: 0.7915 (m-30) cc_final: 0.7432 (t0) REVERT: J 172 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6648 (mp0) REVERT: J 511 ILE cc_start: 0.8491 (mt) cc_final: 0.8120 (pt) REVERT: K 140 TYR cc_start: 0.7131 (t80) cc_final: 0.6823 (t80) REVERT: K 178 ASN cc_start: 0.6666 (m110) cc_final: 0.6199 (t0) REVERT: K 310 MET cc_start: 0.3899 (mmp) cc_final: 0.3395 (mtp) REVERT: K 338 ARG cc_start: 0.6374 (ptt-90) cc_final: 0.6151 (pmt-80) REVERT: K 417 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8352 (tt) REVERT: K 446 GLU cc_start: 0.8019 (tt0) cc_final: 0.7412 (mm-30) REVERT: K 504 MET cc_start: 0.7822 (ttm) cc_final: 0.7441 (ttm) REVERT: L 119 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8269 (mp0) REVERT: L 145 THR cc_start: 0.8426 (m) cc_final: 0.8049 (p) REVERT: L 404 LYS cc_start: 0.6810 (ptpp) cc_final: 0.6502 (tmtt) REVERT: L 476 LYS cc_start: 0.8962 (tttt) cc_final: 0.8612 (ttmm) REVERT: M 10 LYS cc_start: 0.8322 (mttt) cc_final: 0.7831 (pttm) REVERT: M 78 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6472 (p) REVERT: M 116 ASP cc_start: 0.8344 (t0) cc_final: 0.8046 (m-30) REVERT: M 149 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7671 (mp10) REVERT: N 266 MET cc_start: 0.2509 (OUTLIER) cc_final: 0.2049 (mmt) REVERT: N 442 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7707 (tttp) outliers start: 165 outliers final: 118 residues processed: 547 average time/residue: 0.4901 time to fit residues: 470.6588 Evaluate side-chains 517 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 389 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 294 ILE Chi-restraints excluded: chain H residue 386 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 488 ASN Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 399 THR Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 545 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 135 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 417 ILE Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 440 THR Chi-restraints excluded: chain K residue 488 ASN Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 545 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Chi-restraints excluded: chain N residue 545 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 416 optimal weight: 6.9990 chunk 534 optimal weight: 0.0980 chunk 413 optimal weight: 10.0000 chunk 615 optimal weight: 20.0000 chunk 408 optimal weight: 0.3980 chunk 728 optimal weight: 6.9990 chunk 456 optimal weight: 0.4980 chunk 444 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN C 178 ASN C 182 GLN D 100 HIS D 262 ASN E 379 ASN F 499 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN J 178 ASN J 182 GLN ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 HIS K 460 ASN L 379 ASN ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 59022 Z= 0.121 Angle : 0.462 11.635 80066 Z= 0.235 Chirality : 0.037 0.133 9452 Planarity : 0.003 0.047 10410 Dihedral : 4.192 57.209 8172 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.54 % Allowed : 15.67 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7560 helix: 1.75 (0.08), residues: 3982 sheet: -0.71 (0.17), residues: 860 loop : -1.00 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 282 HIS 0.003 0.001 HIS K 96 PHE 0.010 0.001 PHE G 194 TYR 0.020 0.001 TYR B 140 ARG 0.009 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 448 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7891 (ttm-80) REVERT: A 487 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8376 (mp0) REVERT: B 64 GLU cc_start: 0.8527 (tp30) cc_final: 0.7915 (tt0) REVERT: B 116 ASP cc_start: 0.8085 (t0) cc_final: 0.7789 (m-30) REVERT: B 262 ASN cc_start: 0.1906 (m110) cc_final: 0.1686 (m-40) REVERT: B 446 GLU cc_start: 0.8338 (tt0) cc_final: 0.7970 (tm-30) REVERT: B 499 ASN cc_start: 0.8583 (m-40) cc_final: 0.8065 (t0) REVERT: C 170 ASP cc_start: 0.7038 (t70) cc_final: 0.5774 (t0) REVERT: C 222 ARG cc_start: 0.2635 (mtt180) cc_final: 0.2404 (mtt-85) REVERT: C 446 GLU cc_start: 0.7457 (tt0) cc_final: 0.7251 (tp30) REVERT: D 75 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: D 140 TYR cc_start: 0.7271 (t80) cc_final: 0.6915 (t80) REVERT: D 177 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5762 (m) REVERT: D 178 ASN cc_start: 0.6728 (m110) cc_final: 0.6320 (t0) REVERT: D 253 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6535 (tp) REVERT: D 310 MET cc_start: 0.4109 (mmp) cc_final: 0.3659 (mtp) REVERT: D 338 ARG cc_start: 0.6395 (ptt-90) cc_final: 0.6193 (pmt-80) REVERT: D 417 ILE cc_start: 0.8384 (mt) cc_final: 0.8112 (tt) REVERT: D 502 THR cc_start: 0.6028 (OUTLIER) cc_final: 0.5806 (t) REVERT: E 310 MET cc_start: 0.5148 (mmp) cc_final: 0.4924 (mmm) REVERT: E 404 LYS cc_start: 0.6802 (ptpp) cc_final: 0.6457 (tmtt) REVERT: E 476 LYS cc_start: 0.8881 (tttt) cc_final: 0.8586 (ttmm) REVERT: F 78 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6555 (p) REVERT: F 116 ASP cc_start: 0.8131 (t0) cc_final: 0.7782 (m-30) REVERT: F 119 GLU cc_start: 0.8385 (tp30) cc_final: 0.8057 (mm-30) REVERT: F 193 MET cc_start: 0.6668 (ppp) cc_final: 0.6007 (ppp) REVERT: G 144 LEU cc_start: 0.8202 (pp) cc_final: 0.7491 (tp) REVERT: G 193 MET cc_start: 0.5399 (tmm) cc_final: 0.4938 (tpp) REVERT: G 266 MET cc_start: 0.3114 (OUTLIER) cc_final: 0.2709 (mmt) REVERT: G 442 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7615 (tttp) REVERT: H 487 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8352 (mp0) REVERT: I 64 GLU cc_start: 0.8526 (tp30) cc_final: 0.7916 (tt0) REVERT: I 116 ASP cc_start: 0.8087 (t0) cc_final: 0.7793 (m-30) REVERT: I 119 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: I 262 ASN cc_start: 0.1920 (m110) cc_final: 0.1711 (m-40) REVERT: I 337 ASN cc_start: 0.7104 (m-40) cc_final: 0.6467 (p0) REVERT: I 446 GLU cc_start: 0.8355 (tt0) cc_final: 0.7979 (tm-30) REVERT: I 499 ASN cc_start: 0.8589 (m-40) cc_final: 0.8076 (t0) REVERT: J 18 GLN cc_start: 0.8464 (tt0) cc_final: 0.8256 (tt0) REVERT: J 170 ASP cc_start: 0.7041 (t70) cc_final: 0.5775 (t0) REVERT: J 172 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6718 (mp0) REVERT: J 446 GLU cc_start: 0.7309 (tt0) cc_final: 0.7092 (tp30) REVERT: K 75 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7703 (tp30) REVERT: K 140 TYR cc_start: 0.7262 (t80) cc_final: 0.6858 (t80) REVERT: K 177 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.5854 (m) REVERT: K 178 ASN cc_start: 0.6777 (m110) cc_final: 0.6349 (t0) REVERT: K 253 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6484 (tp) REVERT: K 310 MET cc_start: 0.4089 (mmp) cc_final: 0.3630 (mtp) REVERT: K 417 ILE cc_start: 0.8365 (mt) cc_final: 0.8163 (tt) REVERT: K 446 GLU cc_start: 0.8078 (tt0) cc_final: 0.7418 (mm-30) REVERT: K 496 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: K 502 THR cc_start: 0.6060 (OUTLIER) cc_final: 0.5836 (t) REVERT: L 119 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8296 (mp0) REVERT: L 404 LYS cc_start: 0.6793 (ptpp) cc_final: 0.6461 (tmtt) REVERT: L 476 LYS cc_start: 0.8876 (tttt) cc_final: 0.8582 (ttmm) REVERT: L 504 MET cc_start: 0.8710 (ttm) cc_final: 0.8367 (ttp) REVERT: M 78 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6507 (p) REVERT: M 116 ASP cc_start: 0.8121 (t0) cc_final: 0.7818 (m-30) REVERT: M 149 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7522 (mp10) REVERT: M 193 MET cc_start: 0.6765 (ppp) cc_final: 0.6090 (ppp) REVERT: N 144 LEU cc_start: 0.8445 (pp) cc_final: 0.7665 (tp) REVERT: N 266 MET cc_start: 0.3088 (OUTLIER) cc_final: 0.2623 (mmt) REVERT: N 442 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7619 (tttp) outliers start: 95 outliers final: 58 residues processed: 528 average time/residue: 0.5021 time to fit residues: 463.0422 Evaluate side-chains 452 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 380 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 294 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 178 ASN Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 0.8980 chunk 290 optimal weight: 40.0000 chunk 435 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 463 optimal weight: 7.9990 chunk 496 optimal weight: 0.7980 chunk 360 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 572 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS E 379 ASN G 328 GLN H 36 GLN J 182 GLN ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 HIS K 262 ASN K 460 ASN L 379 ASN N 328 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 59022 Z= 0.350 Angle : 0.562 14.193 80066 Z= 0.290 Chirality : 0.041 0.168 9452 Planarity : 0.004 0.049 10410 Dihedral : 4.484 55.074 8172 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.09 % Allowed : 15.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.10), residues: 7560 helix: 1.37 (0.08), residues: 4016 sheet: -0.61 (0.18), residues: 836 loop : -1.08 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 199 HIS 0.006 0.001 HIS F 475 PHE 0.016 0.002 PHE C 491 TYR 0.022 0.002 TYR B 140 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 390 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 THR cc_start: 0.4975 (OUTLIER) cc_final: 0.4723 (m) REVERT: A 418 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7817 (ttm-80) REVERT: A 487 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8397 (mp0) REVERT: B 64 GLU cc_start: 0.8719 (tp30) cc_final: 0.8026 (tt0) REVERT: B 116 ASP cc_start: 0.8232 (t0) cc_final: 0.7841 (m-30) REVERT: B 262 ASN cc_start: 0.1897 (m110) cc_final: 0.1658 (m-40) REVERT: B 446 GLU cc_start: 0.8288 (tt0) cc_final: 0.7891 (tm-30) REVERT: B 499 ASN cc_start: 0.8603 (m-40) cc_final: 0.8089 (t0) REVERT: C 11 ASP cc_start: 0.7920 (m-30) cc_final: 0.7461 (t0) REVERT: C 170 ASP cc_start: 0.6576 (t70) cc_final: 0.6187 (t0) REVERT: C 222 ARG cc_start: 0.2757 (mtt180) cc_final: 0.2390 (mtt-85) REVERT: D 177 VAL cc_start: 0.6400 (OUTLIER) cc_final: 0.6020 (m) REVERT: D 178 ASN cc_start: 0.6932 (m110) cc_final: 0.6463 (t0) REVERT: D 253 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6459 (tp) REVERT: D 310 MET cc_start: 0.4100 (mmp) cc_final: 0.3606 (mtp) REVERT: D 338 ARG cc_start: 0.6501 (ptt-90) cc_final: 0.6244 (pmt-80) REVERT: D 417 ILE cc_start: 0.8678 (mt) cc_final: 0.8374 (tt) REVERT: D 496 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: E 404 LYS cc_start: 0.6855 (ptpp) cc_final: 0.6579 (tmtt) REVERT: E 476 LYS cc_start: 0.8913 (tttt) cc_final: 0.8607 (ttmm) REVERT: F 10 LYS cc_start: 0.8367 (mttt) cc_final: 0.7865 (pttm) REVERT: F 78 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6891 (p) REVERT: F 116 ASP cc_start: 0.8353 (t0) cc_final: 0.8038 (m-30) REVERT: F 119 GLU cc_start: 0.8499 (tp30) cc_final: 0.7937 (tm-30) REVERT: F 193 MET cc_start: 0.6721 (ppp) cc_final: 0.5990 (ppp) REVERT: F 410 TYR cc_start: 0.6235 (m-80) cc_final: 0.6030 (m-80) REVERT: G 193 MET cc_start: 0.5391 (tmm) cc_final: 0.4897 (tpp) REVERT: G 266 MET cc_start: 0.2816 (OUTLIER) cc_final: 0.2367 (mmt) REVERT: H 266 MET cc_start: 0.4823 (mtt) cc_final: 0.4394 (ppp) REVERT: H 487 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8385 (mp0) REVERT: I 64 GLU cc_start: 0.8720 (tp30) cc_final: 0.8027 (tt0) REVERT: I 116 ASP cc_start: 0.8238 (t0) cc_final: 0.7845 (m-30) REVERT: I 262 ASN cc_start: 0.1910 (m110) cc_final: 0.1680 (m-40) REVERT: I 446 GLU cc_start: 0.8306 (tt0) cc_final: 0.7886 (tm-30) REVERT: I 499 ASN cc_start: 0.8605 (m-40) cc_final: 0.8095 (t0) REVERT: J 11 ASP cc_start: 0.7922 (m-30) cc_final: 0.7464 (t0) REVERT: J 172 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6777 (mp0) REVERT: K 140 TYR cc_start: 0.7048 (t80) cc_final: 0.6842 (t80) REVERT: K 177 VAL cc_start: 0.6479 (OUTLIER) cc_final: 0.6072 (m) REVERT: K 178 ASN cc_start: 0.6895 (m110) cc_final: 0.6401 (t0) REVERT: K 253 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6480 (tp) REVERT: K 310 MET cc_start: 0.4177 (mmp) cc_final: 0.3779 (mtp) REVERT: K 417 ILE cc_start: 0.8694 (mt) cc_final: 0.8386 (tt) REVERT: K 446 GLU cc_start: 0.8059 (tt0) cc_final: 0.7382 (mm-30) REVERT: L 119 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8271 (mp0) REVERT: L 404 LYS cc_start: 0.6830 (ptpp) cc_final: 0.6589 (tmtt) REVERT: L 476 LYS cc_start: 0.8917 (tttt) cc_final: 0.8610 (ttmm) REVERT: L 487 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: M 10 LYS cc_start: 0.8357 (mttt) cc_final: 0.7853 (pttm) REVERT: M 78 THR cc_start: 0.7167 (t) cc_final: 0.6903 (p) REVERT: M 116 ASP cc_start: 0.8345 (t0) cc_final: 0.7988 (m-30) REVERT: M 149 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7579 (mp10) REVERT: M 151 GLU cc_start: 0.7656 (tp30) cc_final: 0.7455 (tp30) REVERT: M 193 MET cc_start: 0.6693 (ppp) cc_final: 0.5966 (ppp) REVERT: N 144 LEU cc_start: 0.8507 (pp) cc_final: 0.7720 (tp) REVERT: N 266 MET cc_start: 0.2913 (OUTLIER) cc_final: 0.2454 (mmm) REVERT: N 450 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7654 (mt0) outliers start: 129 outliers final: 105 residues processed: 503 average time/residue: 0.4963 time to fit residues: 440.0094 Evaluate side-chains 487 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 372 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 432 SER Chi-restraints excluded: chain G residue 543 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 294 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 233 ASP Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain I residue 487 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 128 MET Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 488 ASN Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 545 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 334 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 414 VAL Chi-restraints excluded: chain M residue 440 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 90 THR Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Chi-restraints excluded: chain N residue 431 VAL Chi-restraints excluded: chain N residue 545 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 0.9990 chunk 698 optimal weight: 3.9990 chunk 636 optimal weight: 0.6980 chunk 679 optimal weight: 0.8980 chunk 697 optimal weight: 4.9990 chunk 408 optimal weight: 0.5980 chunk 295 optimal weight: 10.0000 chunk 533 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 613 optimal weight: 7.9990 chunk 642 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN D 100 HIS E 100 HIS E 262 ASN E 269 ASN E 379 ASN J 178 ASN J 300 GLN K 100 HIS K 460 ASN L 379 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 59022 Z= 0.127 Angle : 0.458 11.009 80066 Z= 0.234 Chirality : 0.037 0.140 9452 Planarity : 0.003 0.046 10410 Dihedral : 4.049 54.807 8172 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.27 % Allowed : 16.70 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 7560 helix: 1.93 (0.08), residues: 3976 sheet: -0.50 (0.18), residues: 848 loop : -0.93 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 282 HIS 0.002 0.000 HIS H 355 PHE 0.010 0.001 PHE N 194 TYR 0.021 0.001 TYR I 410 ARG 0.004 0.000 ARG K 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 411 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.6228 (mt) cc_final: 0.5972 (pp) REVERT: A 418 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7801 (ttm-80) REVERT: A 487 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8362 (mp0) REVERT: B 64 GLU cc_start: 0.8512 (tp30) cc_final: 0.7893 (tt0) REVERT: B 116 ASP cc_start: 0.8089 (t0) cc_final: 0.7793 (m-30) REVERT: B 193 MET cc_start: 0.7297 (tmm) cc_final: 0.7085 (tmm) REVERT: B 262 ASN cc_start: 0.1980 (m110) cc_final: 0.1535 (m-40) REVERT: B 446 GLU cc_start: 0.8336 (tt0) cc_final: 0.7973 (tm-30) REVERT: B 499 ASN cc_start: 0.8581 (m-40) cc_final: 0.8128 (t0) REVERT: C 170 ASP cc_start: 0.6870 (t70) cc_final: 0.6562 (t0) REVERT: C 222 ARG cc_start: 0.2833 (mtt180) cc_final: 0.2529 (mtt-85) REVERT: D 140 TYR cc_start: 0.6464 (t80) cc_final: 0.6157 (t80) REVERT: D 177 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.6125 (m) REVERT: D 178 ASN cc_start: 0.7016 (m110) cc_final: 0.6526 (t0) REVERT: D 253 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6290 (tp) REVERT: D 310 MET cc_start: 0.4239 (mmp) cc_final: 0.3827 (mtp) REVERT: D 338 ARG cc_start: 0.6551 (ptt-90) cc_final: 0.6315 (pmt-80) REVERT: D 417 ILE cc_start: 0.8434 (mt) cc_final: 0.8220 (tt) REVERT: D 446 GLU cc_start: 0.8058 (tt0) cc_final: 0.7460 (mm-30) REVERT: E 404 LYS cc_start: 0.6822 (ptpp) cc_final: 0.6540 (tmtt) REVERT: E 476 LYS cc_start: 0.8892 (tttt) cc_final: 0.8620 (ttmm) REVERT: F 10 LYS cc_start: 0.8231 (mttt) cc_final: 0.7767 (pttm) REVERT: F 78 THR cc_start: 0.6933 (t) cc_final: 0.6666 (p) REVERT: F 116 ASP cc_start: 0.8141 (t0) cc_final: 0.7819 (m-30) REVERT: F 119 GLU cc_start: 0.8386 (tp30) cc_final: 0.8073 (mm-30) REVERT: F 405 GLU cc_start: 0.8498 (tp30) cc_final: 0.8288 (pp20) REVERT: G 144 LEU cc_start: 0.8251 (pp) cc_final: 0.7560 (tp) REVERT: G 193 MET cc_start: 0.5398 (tmm) cc_final: 0.4916 (tpp) REVERT: G 266 MET cc_start: 0.3124 (OUTLIER) cc_final: 0.2724 (mmt) REVERT: G 310 MET cc_start: 0.6394 (mmp) cc_final: 0.5410 (mtp) REVERT: G 450 GLN cc_start: 0.8102 (mm110) cc_final: 0.7695 (mp10) REVERT: H 266 MET cc_start: 0.4274 (mtt) cc_final: 0.3891 (ppp) REVERT: H 487 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8348 (mp0) REVERT: H 528 THR cc_start: 0.8789 (m) cc_final: 0.8510 (p) REVERT: I 64 GLU cc_start: 0.8511 (tp30) cc_final: 0.7893 (tt0) REVERT: I 116 ASP cc_start: 0.8091 (t0) cc_final: 0.7786 (m-30) REVERT: I 193 MET cc_start: 0.7132 (tmm) cc_final: 0.6897 (tmm) REVERT: I 262 ASN cc_start: 0.1988 (m110) cc_final: 0.1556 (m-40) REVERT: I 446 GLU cc_start: 0.8308 (tt0) cc_final: 0.7942 (tm-30) REVERT: I 499 ASN cc_start: 0.8587 (m-40) cc_final: 0.8103 (t0) REVERT: J 18 GLN cc_start: 0.8437 (tt0) cc_final: 0.8216 (tt0) REVERT: J 170 ASP cc_start: 0.7004 (t70) cc_final: 0.6651 (t0) REVERT: J 446 GLU cc_start: 0.7315 (tt0) cc_final: 0.7098 (tp30) REVERT: K 140 TYR cc_start: 0.6909 (t80) cc_final: 0.6606 (t80) REVERT: K 177 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6096 (m) REVERT: K 178 ASN cc_start: 0.6968 (m110) cc_final: 0.6478 (t0) REVERT: K 253 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6271 (tp) REVERT: K 310 MET cc_start: 0.4260 (mmp) cc_final: 0.3832 (mtp) REVERT: K 417 ILE cc_start: 0.8479 (mt) cc_final: 0.8266 (tt) REVERT: K 446 GLU cc_start: 0.8071 (tt0) cc_final: 0.7490 (mm-30) REVERT: K 496 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: L 404 LYS cc_start: 0.6806 (ptpp) cc_final: 0.6547 (tmtt) REVERT: L 476 LYS cc_start: 0.8880 (tttt) cc_final: 0.8605 (ttmm) REVERT: L 504 MET cc_start: 0.8702 (ttm) cc_final: 0.8367 (ttp) REVERT: M 10 LYS cc_start: 0.8216 (mttt) cc_final: 0.7754 (pttm) REVERT: M 78 THR cc_start: 0.6886 (OUTLIER) cc_final: 0.6626 (p) REVERT: M 116 ASP cc_start: 0.8137 (t0) cc_final: 0.7839 (m-30) REVERT: M 149 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7515 (mp10) REVERT: M 410 TYR cc_start: 0.6485 (m-80) cc_final: 0.6283 (m-80) REVERT: N 144 LEU cc_start: 0.8555 (pp) cc_final: 0.7787 (tp) REVERT: N 266 MET cc_start: 0.3093 (OUTLIER) cc_final: 0.2637 (mmt) REVERT: N 310 MET cc_start: 0.6388 (mmp) cc_final: 0.5406 (mtp) REVERT: N 450 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7598 (mp10) outliers start: 78 outliers final: 58 residues processed: 476 average time/residue: 0.5297 time to fit residues: 444.2016 Evaluate side-chains 455 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 389 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 128 MET Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 545 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 9.9990 chunk 445 optimal weight: 7.9990 chunk 718 optimal weight: 0.7980 chunk 438 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 499 optimal weight: 2.9990 chunk 753 optimal weight: 0.4980 chunk 693 optimal weight: 0.0980 chunk 599 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 182 GLN D 100 HIS E 100 HIS ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 HIS M 355 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 59022 Z= 0.156 Angle : 0.468 11.876 80066 Z= 0.239 Chirality : 0.037 0.143 9452 Planarity : 0.003 0.046 10410 Dihedral : 3.985 53.776 8172 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.41 % Allowed : 16.53 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 7560 helix: 1.97 (0.08), residues: 3982 sheet: -0.42 (0.18), residues: 848 loop : -0.89 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 199 HIS 0.003 0.001 HIS J 355 PHE 0.010 0.001 PHE N 194 TYR 0.019 0.001 TYR I 410 ARG 0.003 0.000 ARG K 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15120 Ramachandran restraints generated. 7560 Oldfield, 0 Emsley, 7560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 407 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.6229 (mt) cc_final: 0.5970 (pp) REVERT: A 344 THR cc_start: 0.4911 (OUTLIER) cc_final: 0.4609 (m) REVERT: A 418 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7787 (ttm-80) REVERT: A 487 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8372 (mp0) REVERT: B 64 GLU cc_start: 0.8543 (tp30) cc_final: 0.7928 (tt0) REVERT: B 116 ASP cc_start: 0.8087 (t0) cc_final: 0.7770 (m-30) REVERT: B 262 ASN cc_start: 0.1860 (m110) cc_final: 0.1652 (m-40) REVERT: B 305 MET cc_start: 0.6281 (ttt) cc_final: 0.5856 (mmm) REVERT: B 446 GLU cc_start: 0.8260 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 499 ASN cc_start: 0.8573 (m-40) cc_final: 0.8131 (t0) REVERT: C 170 ASP cc_start: 0.6846 (t70) cc_final: 0.6542 (t0) REVERT: C 222 ARG cc_start: 0.2772 (mtt180) cc_final: 0.2530 (mtt-85) REVERT: D 140 TYR cc_start: 0.6434 (t80) cc_final: 0.6134 (t80) REVERT: D 177 VAL cc_start: 0.6615 (OUTLIER) cc_final: 0.6197 (m) REVERT: D 178 ASN cc_start: 0.7020 (m110) cc_final: 0.6586 (t0) REVERT: D 310 MET cc_start: 0.4224 (mmp) cc_final: 0.3790 (mtp) REVERT: D 338 ARG cc_start: 0.6485 (ptt-90) cc_final: 0.6255 (pmt-80) REVERT: D 417 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8294 (tt) REVERT: D 446 GLU cc_start: 0.8046 (tt0) cc_final: 0.7464 (mm-30) REVERT: D 519 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7769 (pt) REVERT: E 404 LYS cc_start: 0.6858 (ptpp) cc_final: 0.6574 (tmtt) REVERT: E 476 LYS cc_start: 0.8951 (tttt) cc_final: 0.8706 (ttmm) REVERT: F 10 LYS cc_start: 0.8267 (mttt) cc_final: 0.7776 (pttm) REVERT: F 78 THR cc_start: 0.7039 (t) cc_final: 0.6812 (p) REVERT: F 116 ASP cc_start: 0.8165 (t0) cc_final: 0.7839 (m-30) REVERT: F 119 GLU cc_start: 0.8417 (tp30) cc_final: 0.8129 (mm-30) REVERT: F 405 GLU cc_start: 0.8426 (tp30) cc_final: 0.8205 (pp20) REVERT: G 144 LEU cc_start: 0.8278 (pp) cc_final: 0.7586 (tp) REVERT: G 193 MET cc_start: 0.5350 (tmm) cc_final: 0.4855 (tpp) REVERT: G 266 MET cc_start: 0.3101 (OUTLIER) cc_final: 0.2689 (mmt) REVERT: G 310 MET cc_start: 0.6373 (mmp) cc_final: 0.5376 (mtp) REVERT: G 450 GLN cc_start: 0.8098 (mm110) cc_final: 0.7685 (mp10) REVERT: H 266 MET cc_start: 0.4041 (mtt) cc_final: 0.3803 (ppp) REVERT: H 487 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8371 (mp0) REVERT: H 528 THR cc_start: 0.8918 (m) cc_final: 0.8598 (p) REVERT: I 64 GLU cc_start: 0.8546 (tp30) cc_final: 0.7930 (tt0) REVERT: I 116 ASP cc_start: 0.8083 (t0) cc_final: 0.7761 (m-30) REVERT: I 184 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7282 (tm-30) REVERT: I 193 MET cc_start: 0.7132 (tmm) cc_final: 0.6908 (tmm) REVERT: I 262 ASN cc_start: 0.1868 (m110) cc_final: 0.1648 (m-40) REVERT: I 305 MET cc_start: 0.6288 (ttt) cc_final: 0.5860 (mmm) REVERT: I 446 GLU cc_start: 0.8272 (tt0) cc_final: 0.7918 (tm-30) REVERT: I 499 ASN cc_start: 0.8578 (m-40) cc_final: 0.8131 (t0) REVERT: J 170 ASP cc_start: 0.7048 (t70) cc_final: 0.6684 (t0) REVERT: J 446 GLU cc_start: 0.7383 (tt0) cc_final: 0.7154 (tp30) REVERT: K 140 TYR cc_start: 0.6934 (t80) cc_final: 0.6628 (t80) REVERT: K 177 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6212 (m) REVERT: K 178 ASN cc_start: 0.7063 (m110) cc_final: 0.6604 (t0) REVERT: K 253 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6260 (tp) REVERT: K 310 MET cc_start: 0.4220 (mmp) cc_final: 0.3799 (mtp) REVERT: K 417 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8308 (tt) REVERT: K 446 GLU cc_start: 0.8066 (tt0) cc_final: 0.7494 (mm-30) REVERT: K 496 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: K 519 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7764 (pt) REVERT: L 404 LYS cc_start: 0.6787 (ptpp) cc_final: 0.6502 (tmtt) REVERT: L 476 LYS cc_start: 0.8951 (tttt) cc_final: 0.8703 (ttmm) REVERT: M 10 LYS cc_start: 0.8253 (mttt) cc_final: 0.7763 (pttm) REVERT: M 78 THR cc_start: 0.7034 (t) cc_final: 0.6809 (p) REVERT: M 116 ASP cc_start: 0.8145 (t0) cc_final: 0.7872 (m-30) REVERT: M 149 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7507 (mp10) REVERT: M 151 GLU cc_start: 0.7674 (tp30) cc_final: 0.7471 (tp30) REVERT: M 410 TYR cc_start: 0.6728 (m-80) cc_final: 0.6501 (m-80) REVERT: N 144 LEU cc_start: 0.8548 (pp) cc_final: 0.7786 (tp) REVERT: N 266 MET cc_start: 0.3072 (OUTLIER) cc_final: 0.2656 (mmt) REVERT: N 310 MET cc_start: 0.6413 (mmp) cc_final: 0.5380 (mtp) REVERT: N 450 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7580 (mp10) outliers start: 87 outliers final: 69 residues processed: 480 average time/residue: 0.5038 time to fit residues: 424.7945 Evaluate side-chains 480 residues out of total 6452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 400 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 543 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 385 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 128 MET Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 545 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 417 ILE Chi-restraints excluded: chain K residue 496 ASP Chi-restraints excluded: chain K residue 498 LEU Chi-restraints excluded: chain K residue 519 ILE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 290 VAL Chi-restraints excluded: chain L residue 545 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 178 ASN Chi-restraints excluded: chain N residue 180 GLU Chi-restraints excluded: chain N residue 266 MET Chi-restraints excluded: chain N residue 425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 2.9990 chunk 476 optimal weight: 6.9990 chunk 638 optimal weight: 0.4980 chunk 183 optimal weight: 0.6980 chunk 553 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 600 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 616 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN D 100 HIS ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 HIS L 262 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.188637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144174 restraints weight = 92791.791| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.78 r_work: 0.3320 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 59022 Z= 0.138 Angle : 0.453 11.219 80066 Z= 0.232 Chirality : 0.037 0.144 9452 Planarity : 0.003 0.045 10410 Dihedral : 3.874 52.524 8172 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.46 % Allowed : 16.66 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.10), residues: 7560 helix: 2.08 (0.08), residues: 3984 sheet: -0.34 (0.18), residues: 848 loop : -0.83 (0.12), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 199 HIS 0.003 0.000 HIS C 96 PHE 0.011 0.001 PHE N 194 TYR 0.020 0.001 TYR F 410 ARG 0.004 0.000 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10599.39 seconds wall clock time: 188 minutes 12.77 seconds (11292.77 seconds total)