Starting phenix.real_space_refine on Sat Dec 16 12:36:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2z_9334/12_2023/6n2z_9334_updated.pdb" } resolution = 3.0 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= 0.009 sd= 0.211 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 22297 2.51 5 N 6105 2.21 5 O 6537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b2 ARG 40": "NH1" <-> "NH2" Residue "b1 ARG 40": "NH1" <-> "NH2" Residue "a ARG 39": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "c7 ARG 36": "NH1" <-> "NH2" Residue "c9 ARG 36": "NH1" <-> "NH2" Residue "c0 ARG 36": "NH1" <-> "NH2" Residue "c0 ARG 72": "NH1" <-> "NH2" Residue "c1 ARG 36": "NH1" <-> "NH2" Residue "c2 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 36": "NH1" <-> "NH2" Residue "c3 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c4 ARG 36": "NH1" <-> "NH2" Residue "c5 ARG 29": "NH1" <-> "NH2" Residue "c5 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 36": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 333": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I ARG 171": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35051 Number of models: 1 Model: "" Number of chains: 27 Chain: "b2" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 856 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 1, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'ASN:plan1': 2, 'UNK:plan-1': 17, 'ASP:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "b1" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 890 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 14, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 27, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 238 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3806 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 475} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3725 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3833 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3618 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3578 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3614 Classifications: {'peptide': 471} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2205 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 927 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "I" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1314 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.18, per 1000 atoms: 0.52 Number of scatterers: 35051 At special positions: 0 Unit cell: (117.66, 135.68, 227.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 Mg 4 11.99 O 6537 8.00 N 6105 7.00 C 22297 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.48 Conformation dependent library (CDL) restraints added in 6.5 seconds 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 28 sheets defined 53.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.17 Creating SS restraints... Processing helix chain 'b2' and resid 11 through 139 removed outlier: 5.289A pdb=" N GLNb2 31 " --> pdb=" O LYSb2 27 " (cutoff:3.500A) Proline residue: b2 32 - end of helix removed outlier: 3.724A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) Processing helix chain 'b2' and resid 601 through 615 Processing helix chain 'b1' and resid 10 through 142 removed outlier: 3.621A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix Processing helix chain 'b1' and resid 146 through 162 removed outlier: 3.722A pdb=" N ARGb1 150 " --> pdb=" O GLUb1 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 37 Processing helix chain 'a' and resid 49 through 66 Processing helix chain 'a' and resid 69 through 72 No H-bonds generated for 'chain 'a' and resid 69 through 72' Processing helix chain 'a' and resid 74 through 95 removed outlier: 4.056A pdb=" N THR a 77 " --> pdb=" O ARG a 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY a 79 " --> pdb=" O LEU a 76 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL a 80 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR a 81 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE a 83 " --> pdb=" O VAL a 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET a 84 " --> pdb=" O THR a 81 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL a 86 " --> pdb=" O ILE a 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL a 88 " --> pdb=" O TYR a 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU a 92 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY a 93 " --> pdb=" O ASN a 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU a 94 " --> pdb=" O MET a 91 " (cutoff:3.500A) Proline residue: a 95 - end of helix Processing helix chain 'a' and resid 113 through 129 Processing helix chain 'a' and resid 153 through 190 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 200 through 233 Processing helix chain 'c7' and resid 3 through 36 Processing helix chain 'c7' and resid 38 through 71 removed outlier: 3.834A pdb=" N ARGc7 41 " --> pdb=" O PROc7 38 " (cutoff:3.500A) Proline residue: c7 42 - end of helix removed outlier: 4.381A pdb=" N THRc7 46 " --> pdb=" O VALc7 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THRc7 47 " --> pdb=" O LEUc7 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VALc7 55 " --> pdb=" O VALc7 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLUc7 56 " --> pdb=" O ALAc7 53 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEUc7 58 " --> pdb=" O VALc7 55 " (cutoff:3.500A) Proline residue: c7 59 - end of helix removed outlier: 3.507A pdb=" N PHEc7 67 " --> pdb=" O VALc7 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLYc7 71 " --> pdb=" O ILEc7 68 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 36 Processing helix chain 'c8' and resid 38 through 55 removed outlier: 3.523A pdb=" N ARGc8 41 " --> pdb=" O PROc8 38 " (cutoff:3.500A) Proline residue: c8 42 - end of helix removed outlier: 3.696A pdb=" N THRc8 47 " --> pdb=" O LEUc8 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEc8 50 " --> pdb=" O THRc8 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAc8 53 " --> pdb=" O ILEc8 50 " (cutoff:3.500A) Processing helix chain 'c8' and resid 57 through 71 Processing helix chain 'c9' and resid 3 through 36 Processing helix chain 'c9' and resid 38 through 71 removed outlier: 3.781A pdb=" N ARGc9 41 " --> pdb=" O PROc9 38 " (cutoff:3.500A) Proline residue: c9 42 - end of helix removed outlier: 3.517A pdb=" N THRc9 47 " --> pdb=" O LEUc9 44 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALAc9 57 " --> pdb=" O LEUc9 54 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEUc9 58 " --> pdb=" O VALc9 55 " (cutoff:3.500A) Proline residue: c9 59 - end of helix Processing helix chain 'c0' and resid 3 through 36 Processing helix chain 'c0' and resid 38 through 71 removed outlier: 3.973A pdb=" N ARGc0 41 " --> pdb=" O PROc0 38 " (cutoff:3.500A) Proline residue: c0 42 - end of helix removed outlier: 3.512A pdb=" N THRc0 47 " --> pdb=" O LEUc0 44 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N METc0 48 " --> pdb=" O GLNc0 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALc0 52 " --> pdb=" O PHEc0 49 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLUc0 56 " --> pdb=" O ALAc0 53 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEUc0 58 " --> pdb=" O VALc0 55 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.828A pdb=" N GLYc0 71 " --> pdb=" O ILEc0 68 " (cutoff:3.500A) Processing helix chain 'c1' and resid 4 through 36 Processing helix chain 'c1' and resid 38 through 71 removed outlier: 3.597A pdb=" N ARGc1 41 " --> pdb=" O PROc1 38 " (cutoff:3.500A) Proline residue: c1 42 - end of helix removed outlier: 3.602A pdb=" N THRc1 47 " --> pdb=" O LEUc1 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILEc1 50 " --> pdb=" O THRc1 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALAc1 53 " --> pdb=" O ILEc1 50 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALAc1 57 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEUc1 58 " --> pdb=" O VALc1 55 " (cutoff:3.500A) Proline residue: c1 59 - end of helix removed outlier: 3.976A pdb=" N PHEc1 67 " --> pdb=" O VALc1 64 " (cutoff:3.500A) Processing helix chain 'c2' and resid 4 through 36 Processing helix chain 'c2' and resid 41 through 71 removed outlier: 4.290A pdb=" N LEUc2 58 " --> pdb=" O LEUc2 54 " (cutoff:3.500A) Proline residue: c2 59 - end of helix Processing helix chain 'c3' and resid 4 through 36 Processing helix chain 'c3' and resid 41 through 71 removed outlier: 4.372A pdb=" N LEUc3 58 " --> pdb=" O LEUc3 54 " (cutoff:3.500A) Proline residue: c3 59 - end of helix removed outlier: 3.635A pdb=" N GLYc3 71 " --> pdb=" O PHEc3 67 " (cutoff:3.500A) Processing helix chain 'c4' and resid 3 through 36 Processing helix chain 'c4' and resid 38 through 71 Proline residue: c4 42 - end of helix removed outlier: 3.633A pdb=" N THRc4 47 " --> pdb=" O LEUc4 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUc4 56 " --> pdb=" O ALAc4 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAc4 57 " --> pdb=" O LEUc4 54 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEUc4 58 " --> pdb=" O VALc4 55 " (cutoff:3.500A) Proline residue: c4 59 - end of helix removed outlier: 3.510A pdb=" N LEUc4 70 " --> pdb=" O PHEc4 67 " (cutoff:3.500A) Processing helix chain 'c5' and resid 4 through 36 Processing helix chain 'c5' and resid 38 through 71 Proline residue: c5 42 - end of helix removed outlier: 3.615A pdb=" N THRc5 47 " --> pdb=" O LEUc5 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILEc5 50 " --> pdb=" O THRc5 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAc5 53 " --> pdb=" O ILEc5 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLUc5 56 " --> pdb=" O ALAc5 53 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALAc5 57 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEUc5 58 " --> pdb=" O VALc5 55 " (cutoff:3.500A) Proline residue: c5 59 - end of helix removed outlier: 3.965A pdb=" N GLYc5 71 " --> pdb=" O ILEc5 68 " (cutoff:3.500A) Processing helix chain 'c6' and resid 4 through 36 Processing helix chain 'c6' and resid 41 through 70 removed outlier: 3.827A pdb=" N THRc6 47 " --> pdb=" O VALc6 43 " (cutoff:3.500A) Proline residue: c6 59 - end of helix Processing helix chain 'B' and resid 4 through 23 removed outlier: 4.820A pdb=" N SER B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.380A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 4.042A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.520A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.713A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 419 removed outlier: 3.794A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.631A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 465 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 467 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.589A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.113A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.993A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 removed outlier: 3.753A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.298A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 347 through 350 No H-bonds generated for 'chain 'C' and resid 347 through 350' Processing helix chain 'C' and resid 375 through 392 removed outlier: 5.047A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 420 removed outlier: 4.180A pdb=" N ARG C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.677A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 465 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.618A pdb=" N ALA C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.647A pdb=" N GLN A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.570A pdb=" N ASN A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 4.016A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.853A pdb=" N ALA A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 4.405A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.968A pdb=" N SER A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 removed outlier: 3.963A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.637A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 466 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 4.046A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 222 through 242 removed outlier: 5.183A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.866A pdb=" N ALA E 260 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 265 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA E 266 " --> pdb=" O GLU E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.520A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 4.254A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 386 removed outlier: 3.608A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 409 removed outlier: 3.940A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.650A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 421 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.593A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.902A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.532A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 289 Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 321 removed outlier: 3.610A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 361 through 387 removed outlier: 4.554A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 4.159A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 removed outlier: 3.896A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR F 421 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 195 through 205 WARNING: missing atoms! Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.705A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.589A pdb=" N VAL D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.565A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 319 No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 361 through 386 removed outlier: 5.050A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 410 removed outlier: 4.197A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.734A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'G' and resid 4 through 57 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.900A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 Processing helix chain 'G' and resid 209 through 282 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 90 through 130 removed outlier: 3.738A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 20 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 43 through 48 Processing helix chain 'I' and resid 55 through 65 Processing helix chain 'I' and resid 71 through 82 Processing helix chain 'I' and resid 86 through 104 removed outlier: 3.654A pdb=" N VAL I 89 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Proline residue: I 90 - end of helix removed outlier: 3.539A pdb=" N GLN I 95 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG I 104 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 removed outlier: 4.293A pdb=" N GLN I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 175 Processing sheet with id= A, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= B, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.857A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.550A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 221 through 226 removed outlier: 8.815A pdb=" N ILE B 222 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS B 255 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 194 " --> pdb=" O HIS B 255 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 198 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 261 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.521A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 76 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY C 61 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.951A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.938A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.713A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.398A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG A 93 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 91 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.341A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.701A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 319 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 8.428A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.373A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG E 60 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= P, first strand: chain 'E' and resid 94 through 96 removed outlier: 4.001A pdb=" N ARG E 94 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL E 184 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU E 248 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA E 186 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE E 250 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL E 188 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP E 252 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER E 299 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 249 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR E 301 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE E 251 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 303 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA E 327 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE E 157 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR E 329 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.427A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 60 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= S, first strand: chain 'F' and resid 302 through 305 removed outlier: 7.060A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 211 through 216 removed outlier: 6.827A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL F 184 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU F 248 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA F 186 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE F 250 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 188 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP F 252 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER F 299 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU F 249 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 301 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE F 251 " --> pdb=" O THR F 301 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.314A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= W, first strand: chain 'D' and resid 327 through 330 removed outlier: 7.367A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 113 through 118 removed outlier: 6.329A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 189 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 41 through 43 Processing sheet with id= Z, first strand: chain 'H' and resid 49 through 52 Processing sheet with id= AA, first strand: chain 'H' and resid 4 through 9 removed outlier: 3.695A pdb=" N TYR H 16 " --> pdb=" O VAL H 8 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 137 through 143 removed outlier: 3.598A pdb=" N SER I 113 " --> pdb=" O ILE I 143 " (cutoff:3.500A) 1853 hydrogen bonds defined for protein. 4956 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: 12.53 Time building geometry restraints manager: 15.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5934 1.31 - 1.43: 8455 1.43 - 1.56: 20990 1.56 - 1.69: 18 1.69 - 1.81: 191 Bond restraints: 35588 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.51e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 ... (remaining 35583 not shown) Histogram of bond angle deviations from ideal: 96.16 - 104.11: 524 104.11 - 112.07: 17100 112.07 - 120.02: 15527 120.02 - 127.98: 14974 127.98 - 135.93: 221 Bond angle restraints: 48346 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 119.83 20.04 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 123.48 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.07 15.76 1.00e+00 1.00e+00 2.48e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 122.40 14.43 1.00e+00 1.00e+00 2.08e+02 ... (remaining 48341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 20833 21.85 - 43.70: 602 43.70 - 65.54: 39 65.54 - 87.39: 26 87.39 - 109.24: 1 Dihedral angle restraints: 21501 sinusoidal: 8120 harmonic: 13381 Sorted by residual: dihedral pdb=" CA ASP G 136 " pdb=" C ASP G 136 " pdb=" N ILE G 137 " pdb=" CA ILE G 137 " ideal model delta harmonic sigma weight residual -180.00 -141.76 -38.24 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA ASP E 394 " pdb=" C ASP E 394 " pdb=" N GLU E 395 " pdb=" CA GLU E 395 " ideal model delta harmonic sigma weight residual -180.00 -146.38 -33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA SER A 400 " pdb=" C SER A 400 " pdb=" N ASP A 401 " pdb=" CA ASP A 401 " ideal model delta harmonic sigma weight residual 180.00 146.81 33.19 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 21498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5013 0.095 - 0.189: 730 0.189 - 0.284: 38 0.284 - 0.378: 4 0.378 - 0.473: 2 Chirality restraints: 5787 Sorted by residual: chirality pdb=" CA TYR F 277 " pdb=" N TYR F 277 " pdb=" C TYR F 277 " pdb=" CB TYR F 277 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CG LEU C 313 " pdb=" CB LEU C 313 " pdb=" CD1 LEU C 313 " pdb=" CD2 LEU C 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 5784 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUc8 58 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PROc8 59 " -0.133 5.00e-02 4.00e+02 pdb=" CA PROc8 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PROc8 59 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUc0 58 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PROc0 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROc0 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROc0 59 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLNc6 37 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PROc6 38 " -0.127 5.00e-02 4.00e+02 pdb=" CA PROc6 38 " 0.038 5.00e-02 4.00e+02 pdb=" CD PROc6 38 " 0.040 5.00e-02 4.00e+02 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 6 1.69 - 2.49: 175 2.49 - 3.30: 39426 3.30 - 4.10: 89701 4.10 - 4.90: 166164 Warning: very small nonbonded interaction distances. Nonbonded interactions: 295472 Sorted by model distance: nonbonded pdb=" OE2 GLUc5 39 " pdb=" O PRO H 36 " model vdw 0.890 3.040 nonbonded pdb=" CD GLUc5 39 " pdb=" O PRO H 36 " model vdw 0.895 3.270 nonbonded pdb=" OE2 GLUc5 39 " pdb=" C PRO H 36 " model vdw 1.394 3.270 nonbonded pdb=" OH TYR E 277 " pdb=" OD2 ASP E 315 " model vdw 1.587 2.440 nonbonded pdb=" O PHEc3 65 " pdb=" CD1 TYRc3 69 " model vdw 1.610 3.340 ... (remaining 295467 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 8 through 18 and (name N or name CA or name C or name O o \ r name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name CB )) or resid 40 through 352 or (resid 353 and (name N or name CA o \ r name C or name CB or name CG1 or name CG2)) or resid 354 through 393 or (resid \ 394 and (name N or name CA or name C or name CB )) or resid 395 through 396 or \ (resid 397 through 398 and (name N or name CA or name C or name O or name CB )) \ or resid 399 through 402 or (resid 403 through 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 450 or (resid 451 and (name N o \ r name CA or name C or name O or name CB )) or resid 452 through 484 or (resid 4 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 486 through \ 495 or (resid 496 and (name N or name CA or name C or name O or name CB )) or r \ esid 497 through 501 or resid 600 through 601)) selection = (chain 'B' and ((resid 8 through 18 and (name N or name CA or name C or name O o \ r name CB )) or resid 19 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 352 or (resid 353 and (name N o \ r name CA or name C or name CB or name CG1 or name CG2)) or resid 354 through 39 \ 6 or (resid 397 through 398 and (name N or name CA or name C or name O or name C \ B )) or resid 399 through 405 or (resid 406 through 408 and (name N or name CA o \ r name C or name O or name CB )) or resid 409 through 450 or (resid 451 and (nam \ e N or name CA or name C or name O or name CB )) or resid 452 through 484 or (re \ sid 485 and (name N or name CA or name C or name O or name CB )) or resid 486 th \ rough 495 or (resid 496 and (name N or name CA or name C or name O or name CB )) \ or resid 497 through 501 or resid 600 through 601)) selection = (chain 'C' and (resid 8 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 38 or (resid 39 and (name N or name \ CA or name C or name CB )) or resid 40 through 187 or (resid 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name CB )) or resid 395 through 501 or res \ id 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 381 or (resid 382 and (name N or \ name CA or name C or name O or name CB )) or resid 383 through 388 or (resid 38 \ 9 through 392 and (name N or name CA or name C or name O or name CB )) or resid \ 393 or (resid 394 through 397 and (name N or name CA or name C or name O or name \ CB )) or resid 398 through 430 or (resid 431 and (name N or name CA or name C o \ r name O or name CB )) or resid 432 through 468 or (resid 469 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 130 or (res \ id 131 and (name N or name CA or name C or name O or name CB )) or resid 132 thr \ ough 195 or (resid 196 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2)) or resid 197 through 208 or (resid 209 and (name N or na \ me CA or name C or name CB or name OG )) or resid 210 through 296 or (resid 297 \ and (name N or name CA or name C or name CB or name CG or name CD or name CE or \ name NZ )) or resid 298 through 381 or (resid 382 and (name N or name CA or name \ C or name O or name CB )) or resid 383 through 388 or (resid 389 through 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 39 \ 4 through 397 and (name N or name CA or name C or name O or name CB )) or resid \ 398 through 420 or (resid 421 and (name N or name CA or name C or name CB or nam \ e OG1 or name CG2)) or (resid 422 and (name N or name CA or name C )) or resid 4 \ 23 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 468 or (resid 469 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'F' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 195 or (res \ id 196 and (name N or name CA or name C or name CB or name CG or name OD1 or nam \ e ND2)) or resid 197 through 208 or (resid 209 and (name N or name CA or name C \ or name CB or name OG )) or resid 210 through 296 or (resid 297 and (name N or n \ ame CA or name C or name CB or name CG or name CD or name CE or name NZ )) or re \ sid 298 through 420 or (resid 421 and (name N or name CA or name C or name CB or \ name OG1 or name CG2)) or (resid 422 and (name N or name CA or name C )) or res \ id 423 through 469)) } ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 through 140 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 140)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.910 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 92.150 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.200 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 0.117 35588 Z= 0.503 Angle : 1.079 20.037 48346 Z= 0.614 Chirality : 0.063 0.473 5787 Planarity : 0.008 0.077 6254 Dihedral : 10.697 109.241 12921 Min Nonbonded Distance : 0.890 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 0.51 % Allowed : 5.60 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.11), residues: 4642 helix: -1.31 (0.09), residues: 2505 sheet: -1.18 (0.21), residues: 569 loop : -1.96 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 206 HIS 0.020 0.002 HIS F 363 PHE 0.043 0.004 PHEc3 65 TYR 0.034 0.003 TYRc7 69 ARG 0.013 0.001 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 729 time to evaluate : 4.234 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 TARDY: cannot create tardy model for: "VAL C 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 746 average time/residue: 1.5286 time to fit residues: 1361.7578 Evaluate side-chains 472 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 466 time to evaluate : 4.080 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.4162 time to fit residues: 6.8333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 0.7980 chunk 352 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 364 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 271 optimal weight: 0.3980 chunk 422 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 31 GLN b2 35 ASN a 16 ASN a 49 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 HIS ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 23 ASN c4 23 ASN B 186 GLN B 189 GLN B 422 GLN B 425 HIS C 147 GLN C 186 GLN C 189 GLN C 433 GLN C 483 ASN A 18 ASN A 46 ASN A 186 GLN A 189 GLN A 215 HIS A 333 ASN A 345 GLN A 397 GLN A 425 HIS A 488 ASN E 289 GLN E 304 GLN E 330 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 GLN F 28 ASN F 53 HIS F 169 GLN F 196 ASN F 289 GLN F 304 GLN F 375 GLN F 401 HIS D 219 ASN D 253 ASN D 324 HIS D 423 GLN G 50 GLN G 55 ASN G 173 ASN G 174 HIS I 3 GLN I 57 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35588 Z= 0.216 Angle : 0.641 11.101 48346 Z= 0.326 Chirality : 0.045 0.209 5787 Planarity : 0.005 0.082 6254 Dihedral : 6.683 89.277 5170 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 3.77 % Allowed : 12.19 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.97 (0.12), residues: 4642 helix: -0.04 (0.10), residues: 2506 sheet: -0.77 (0.21), residues: 579 loop : -1.42 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 206 HIS 0.008 0.001 HIS D 363 PHE 0.025 0.002 PHE a 212 TYR 0.019 0.001 TYRb1 13 ARG 0.007 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 504 time to evaluate : 4.252 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 132 outliers final: 39 residues processed: 590 average time/residue: 1.4366 time to fit residues: 1028.2670 Evaluate side-chains 486 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 447 time to evaluate : 3.998 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 28 residues processed: 12 average time/residue: 0.5652 time to fit residues: 15.7894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 chunk 456 optimal weight: 0.0030 chunk 376 optimal weight: 4.9990 chunk 419 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN C 113 GLN C 215 HIS A 422 GLN E 28 ASN E 217 GLN E 365 GLN F 28 ASN F 40 ASN D 423 GLN G 33 ASN G 143 GLN G 181 GLN I 21 GLN I 57 GLN I 95 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35588 Z= 0.259 Angle : 0.626 11.185 48346 Z= 0.314 Chirality : 0.046 0.286 5787 Planarity : 0.005 0.053 6254 Dihedral : 6.418 85.452 5170 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 3.46 % Allowed : 14.02 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.12), residues: 4642 helix: 0.48 (0.10), residues: 2506 sheet: -0.67 (0.22), residues: 555 loop : -1.11 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 105 HIS 0.010 0.001 HIS F 363 PHE 0.030 0.002 PHE a 212 TYR 0.021 0.001 TYR G 113 ARG 0.007 0.001 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 486 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 121 outliers final: 60 residues processed: 570 average time/residue: 1.3366 time to fit residues: 931.6659 Evaluate side-chains 514 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 454 time to evaluate : 3.903 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 48 residues processed: 15 average time/residue: 0.6030 time to fit residues: 18.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 46 optimal weight: 40.0000 chunk 201 optimal weight: 0.7980 chunk 284 optimal weight: 0.5980 chunk 424 optimal weight: 3.9990 chunk 449 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c6 45 GLN C 113 GLN C 345 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN G 272 GLN ** I 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35588 Z= 0.273 Angle : 0.623 11.028 48346 Z= 0.311 Chirality : 0.046 0.342 5787 Planarity : 0.004 0.056 6254 Dihedral : 6.270 77.968 5170 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 4.28 % Allowed : 15.39 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.07 (0.12), residues: 4642 helix: 0.71 (0.10), residues: 2515 sheet: -0.63 (0.22), residues: 561 loop : -0.92 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 206 HIS 0.010 0.001 HIS F 363 PHE 0.021 0.002 PHE a 212 TYR 0.018 0.001 TYR A 292 ARG 0.012 0.001 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 462 time to evaluate : 4.084 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 150 outliers final: 68 residues processed: 568 average time/residue: 1.3197 time to fit residues: 923.5209 Evaluate side-chains 509 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 441 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 55 residues processed: 15 average time/residue: 0.5221 time to fit residues: 17.3245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 383 optimal weight: 0.0070 chunk 310 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 229 optimal weight: 1.9990 chunk 403 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 113 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN E 217 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS G 181 GLN G 272 GLN H 38 HIS I 3 GLN ** I 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35588 Z= 0.291 Angle : 0.632 12.806 48346 Z= 0.314 Chirality : 0.046 0.342 5787 Planarity : 0.004 0.052 6254 Dihedral : 6.176 80.319 5170 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 16.19 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.12), residues: 4642 helix: 0.82 (0.10), residues: 2520 sheet: -0.60 (0.22), residues: 582 loop : -0.77 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 206 HIS 0.011 0.001 HIS F 363 PHE 0.042 0.002 PHE a 96 TYR 0.036 0.001 TYR B 438 ARG 0.009 0.001 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 452 time to evaluate : 4.049 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 148 outliers final: 81 residues processed: 554 average time/residue: 1.3816 time to fit residues: 943.1876 Evaluate side-chains 514 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 433 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 64 residues processed: 17 average time/residue: 0.6255 time to fit residues: 21.1707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 0.9990 chunk 404 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 263 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 449 optimal weight: 8.9990 chunk 373 optimal weight: 0.9980 chunk 208 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS C 113 GLN C 345 GLN E 169 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 3 GLN ** I 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN I 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35588 Z= 0.207 Angle : 0.597 13.590 48346 Z= 0.297 Chirality : 0.044 0.330 5787 Planarity : 0.004 0.054 6254 Dihedral : 5.951 80.313 5170 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 3.54 % Allowed : 17.48 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.12), residues: 4642 helix: 0.97 (0.11), residues: 2519 sheet: -0.47 (0.22), residues: 580 loop : -0.67 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 206 HIS 0.006 0.001 HIS F 363 PHE 0.025 0.001 PHE A 463 TYR 0.023 0.001 TYR G 113 ARG 0.005 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 461 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 124 outliers final: 70 residues processed: 554 average time/residue: 1.2251 time to fit residues: 834.4761 Evaluate side-chains 514 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 444 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 59 residues processed: 11 average time/residue: 0.4376 time to fit residues: 11.4771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 256 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 378 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 448 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: