Starting phenix.real_space_refine on Fri Mar 22 22:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n30_9335/03_2024/6n30_9335_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.171 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 22180 2.51 5 N 6069 2.21 5 O 6490 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 "c3 ARG 36": "NH1" <-> "NH2" Residue "c5 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 72": "NH1" <-> "NH2" Residue "c7 ARG 36": "NH1" <-> "NH2" Residue "c8 ARG 36": "NH1" <-> "NH2" Residue "c9 ARG 36": "NH1" <-> "NH2" Residue "c0 ARG 36": "NH1" <-> "NH2" Residue "c1 ARG 29": "NH1" <-> "NH2" Residue "c1 ARG 36": "NH1" <-> "NH2" Residue "c2 ARG 36": "NH1" <-> "NH2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F ARG 435": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 352": "NH1" <-> "NH2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E 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 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 104": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34851 Number of models: 1 Model: "" Number of chains: 27 Chain: "b2" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 854 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 1, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 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: 204 Chain: "b1" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 889 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 478 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: "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: "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: "C" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3736 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3794 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3780 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 475} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3610 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3581 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "E" 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: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2196 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 273} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 924 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "I" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1188 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 139 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: "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: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 16.92, per 1000 atoms: 0.49 Number of scatterers: 34851 At special positions: 0 Unit cell: (127.2, 138.86, 226.84, 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 6490 8.00 N 6069 7.00 C 22180 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.13 Conformation dependent library (CDL) restraints added in 6.0 seconds 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 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: 164 helices and 25 sheets defined 53.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'b2' and resid 11 through 122 removed outlier: 5.288A pdb=" N GLNb2 31 " --> pdb=" O LYSb2 27 " (cutoff:3.500A) Proline residue: b2 32 - end of helix removed outlier: 4.342A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILEb2 48 " --> pdb=" O ILEb2 44 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASPb2 49 " --> pdb=" O ALAb2 45 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLNb2 50 " --> pdb=" O ASNb2 46 " (cutoff:3.500A) Processing helix chain 'b2' and resid 125 through 139 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 removed outlier: 3.743A pdb=" N ALAb1 45 " --> pdb=" O GLUb1 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASNb1 46 " --> pdb=" O GLUb1 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLUb1 47 " --> pdb=" O HISb1 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLUb1 59 " --> pdb=" O ARGb1 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYSb1 60 " --> pdb=" O GLNb1 56 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEUb1 61 " --> pdb=" O GLUb1 57 " (cutoff:3.500A) Processing helix chain 'b1' and resid 146 through 162 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: 3.527A 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: 3.603A 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: 3.978A 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 'c3' and resid 3 through 36 Processing helix chain 'c3' and resid 38 through 71 removed outlier: 3.835A pdb=" N ARGc3 41 " --> pdb=" O PROc3 38 " (cutoff:3.500A) Proline residue: c3 42 - end of helix removed outlier: 4.380A pdb=" N THRc3 46 " --> pdb=" O VALc3 43 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THRc3 47 " --> pdb=" O LEUc3 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VALc3 55 " --> pdb=" O VALc3 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLUc3 56 " --> pdb=" O ALAc3 53 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEUc3 58 " --> pdb=" O VALc3 55 " (cutoff:3.500A) Proline residue: c3 59 - end of helix removed outlier: 3.507A pdb=" N PHEc3 67 " --> pdb=" O VALc3 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLYc3 71 " --> pdb=" O ILEc3 68 " (cutoff:3.500A) Processing helix chain 'c4' and resid 3 through 36 Processing helix chain 'c4' and resid 38 through 55 removed outlier: 3.523A pdb=" N ARGc4 41 " --> pdb=" O PROc4 38 " (cutoff:3.500A) Proline residue: c4 42 - end of helix removed outlier: 3.696A pdb=" N THRc4 47 " --> pdb=" O LEUc4 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEc4 50 " --> pdb=" O THRc4 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAc4 53 " --> pdb=" O ILEc4 50 " (cutoff:3.500A) Processing helix chain 'c4' and resid 57 through 71 Processing helix chain 'c5' and resid 3 through 36 Processing helix chain 'c5' and resid 38 through 71 removed outlier: 3.782A pdb=" N ARGc5 41 " --> pdb=" O PROc5 38 " (cutoff:3.500A) Proline residue: c5 42 - end of helix removed outlier: 3.517A pdb=" N THRc5 47 " --> pdb=" O LEUc5 44 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALAc5 57 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEUc5 58 " --> pdb=" O VALc5 55 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 3 through 36 Processing helix chain 'c6' and resid 38 through 71 removed outlier: 3.973A pdb=" N ARGc6 41 " --> pdb=" O PROc6 38 " (cutoff:3.500A) Proline residue: c6 42 - end of helix removed outlier: 3.513A pdb=" N THRc6 47 " --> pdb=" O LEUc6 44 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N METc6 48 " --> pdb=" O GLNc6 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALc6 52 " --> pdb=" O PHEc6 49 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLUc6 56 " --> pdb=" O ALAc6 53 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEUc6 58 " --> pdb=" O VALc6 55 " (cutoff:3.500A) Proline residue: c6 59 - end of helix removed outlier: 3.828A pdb=" N GLYc6 71 " --> pdb=" O ILEc6 68 " (cutoff:3.500A) Processing helix chain 'c7' and resid 4 through 36 Processing helix chain 'c7' and resid 38 through 71 removed outlier: 3.597A pdb=" N ARGc7 41 " --> pdb=" O PROc7 38 " (cutoff:3.500A) Proline residue: c7 42 - end of helix removed outlier: 3.602A pdb=" N THRc7 47 " --> pdb=" O LEUc7 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILEc7 50 " --> pdb=" O THRc7 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALAc7 53 " --> pdb=" O ILEc7 50 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALAc7 57 " --> pdb=" O LEUc7 54 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEUc7 58 " --> pdb=" O VALc7 55 " (cutoff:3.500A) Proline residue: c7 59 - end of helix removed outlier: 3.976A pdb=" N PHEc7 67 " --> pdb=" O VALc7 64 " (cutoff:3.500A) Processing helix chain 'c8' and resid 4 through 36 Processing helix chain 'c8' and resid 41 through 71 removed outlier: 4.290A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 4 through 36 Processing helix chain 'c9' and resid 41 through 71 removed outlier: 4.373A pdb=" N LEUc9 58 " --> pdb=" O LEUc9 54 " (cutoff:3.500A) Proline residue: c9 59 - end of helix removed outlier: 3.635A pdb=" N GLYc9 71 " --> pdb=" O PHEc9 67 " (cutoff:3.500A) Processing helix chain 'c0' and resid 3 through 36 Processing helix chain 'c0' and resid 38 through 71 Proline residue: c0 42 - end of helix removed outlier: 3.634A pdb=" N THRc0 47 " --> pdb=" O LEUc0 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUc0 56 " --> pdb=" O ALAc0 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAc0 57 " --> pdb=" O LEUc0 54 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEUc0 58 " --> pdb=" O VALc0 55 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.510A pdb=" N LEUc0 70 " --> pdb=" O PHEc0 67 " (cutoff:3.500A) Processing helix chain 'c1' and resid 4 through 36 Processing helix chain 'c1' and resid 38 through 71 Proline residue: c1 42 - end of helix removed outlier: 3.615A pdb=" N THRc1 47 " --> pdb=" O LEUc1 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILEc1 50 " --> pdb=" O THRc1 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALAc1 53 " --> pdb=" O ILEc1 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLUc1 56 " --> pdb=" O ALAc1 53 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALAc1 57 " --> pdb=" O LEUc1 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUc1 58 " --> pdb=" O VALc1 55 " (cutoff:3.500A) Proline residue: c1 59 - end of helix removed outlier: 3.965A pdb=" N GLYc1 71 " --> pdb=" O ILEc1 68 " (cutoff:3.500A) Processing helix chain 'c2' and resid 4 through 36 Processing helix chain 'c2' and resid 41 through 70 removed outlier: 3.827A pdb=" N THRc2 47 " --> pdb=" O VALc2 43 " (cutoff:3.500A) Proline residue: c2 59 - end of helix Processing helix chain 'C' and resid 9 through 18 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: 3.673A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.892A 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 252 Proline residue: C 239 - end of helix removed outlier: 4.301A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 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: 4.522A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.650A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 373 through 377' Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.920A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 419 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 467 removed outlier: 5.185A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 465 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 467 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.855A pdb=" N LYS C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 15 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 187 removed outlier: 4.321A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (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 250 removed outlier: 3.573A pdb=" N LEU A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.021A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 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: 4.419A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.515A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.156A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.651A 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 232 through 236 Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.910A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.868A 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 291 through 298 removed outlier: 3.807A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 373 through 395 removed outlier: 3.844A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 4.531A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 466 removed outlier: 5.035A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 465 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.541A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (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 205 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.939A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.740A pdb=" N GLY F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 288 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 322 Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 379 Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 397 through 409 removed outlier: 3.609A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.792A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 460 through 469 removed outlier: 3.894A pdb=" N ALA F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) 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 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' 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 241 removed outlier: 3.773A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 281 through 289 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 322 removed outlier: 3.764A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 361 through 387 removed outlier: 3.754A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 409 removed outlier: 4.302A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.946A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) 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 462 through 468 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.629A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'E' and resid 222 through 242 removed outlier: 3.695A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 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 287 removed outlier: 3.834A pdb=" N MET E 285 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY E 286 " --> pdb=" O ALA E 282 " (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 319 No H-bonds generated for 'chain 'E' and resid 316 through 319' Processing helix chain 'E' and resid 322 through 324 No H-bonds generated for 'chain 'E' and resid 322 through 324' Processing helix chain 'E' and resid 333 through 337 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: 5.010A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 396 through 409 removed outlier: 4.202A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 459 through 469 Processing helix chain 'G' and resid 4 through 41 Processing helix chain 'G' and resid 43 through 57 removed outlier: 3.866A pdb=" N LYS G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.891A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 150 through 161 removed outlier: 3.838A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 282 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 88 through 130 removed outlier: 3.704A pdb=" N LEU H 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG H 92 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 93 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 94 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 98 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 130 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 21 removed outlier: 3.503A pdb=" N TYR I 10 " --> pdb=" O ILE I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 40 removed outlier: 3.658A pdb=" N ASP I 30 " --> pdb=" O ARG I 26 " (cutoff:3.500A) 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: 3.743A pdb=" N VAL I 89 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Proline residue: I 90 - end of helix removed outlier: 3.528A pdb=" N GLN I 95 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL I 100 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP I 101 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG I 104 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 Processing helix chain 'I' and resid 166 through 175 Processing sheet with id= A, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.184A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'C' and resid 106 through 108 removed outlier: 6.859A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.836A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.445A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.129A pdb=" N MET A 60 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'A' and resid 341 through 344 removed outlier: 7.006A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 312 through 317 removed outlier: 6.155A pdb=" N ILE A 222 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 197 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 224 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLY A 199 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA A 226 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.354A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.126A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 341 through 344 removed outlier: 7.132A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 319 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.600A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 75 through 77 removed outlier: 3.575A pdb=" N GLY F 4 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'F' and resid 327 through 330 removed outlier: 6.731A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.383A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 60 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 327 through 329 removed outlier: 8.755A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 188 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 216 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.366A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 14 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 60 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= T, first strand: chain 'E' and resid 327 through 330 removed outlier: 7.616A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE E 306 " --> pdb=" O GLY E 158 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR E 307 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP E 252 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA E 186 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 113 through 118 removed outlier: 6.321A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 23 through 26 Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 Processing sheet with id= X, first strand: chain 'H' and resid 48 through 51 removed outlier: 3.602A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 62 " --> pdb=" O GLU H 83 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 138 through 143 removed outlier: 6.268A pdb=" N ALA I 107 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU I 141 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA I 109 " --> pdb=" O GLU I 141 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE I 143 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA I 111 " --> pdb=" O ILE I 143 " (cutoff:3.500A) 1868 hydrogen bonds defined for protein. 4917 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: 12.66 Time building geometry restraints manager: 14.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5895 1.29 - 1.42: 8214 1.42 - 1.55: 20938 1.55 - 1.68: 150 1.68 - 1.81: 191 Bond restraints: 35388 Sorted by residual: bond pdb=" N SERb1 130 " pdb=" CA SERb1 130 " ideal model delta sigma weight residual 1.459 1.338 0.121 1.21e-02 6.83e+03 1.01e+02 bond pdb=" CA SERb1 137 " pdb=" C SERb1 137 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.30e-02 5.92e+03 6.75e+01 bond pdb=" N ALAb1 109 " pdb=" CA ALAb1 109 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.19e-02 7.06e+03 6.54e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 ... (remaining 35383 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.09: 556 104.09 - 112.07: 16809 112.07 - 120.05: 16003 120.05 - 128.03: 14478 128.03 - 136.01: 255 Bond angle restraints: 48101 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 119.11 20.76 1.00e+00 1.00e+00 4.31e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.72 20.15 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 125.24 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 48096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 20260 17.42 - 34.85: 896 34.85 - 52.27: 150 52.27 - 69.70: 25 69.70 - 87.12: 18 Dihedral angle restraints: 21349 sinusoidal: 7966 harmonic: 13383 Sorted by residual: dihedral pdb=" CA LEU G 189 " pdb=" C LEU G 189 " pdb=" N PRO G 190 " pdb=" CA PRO G 190 " ideal model delta harmonic sigma weight residual 180.00 104.78 75.22 0 5.00e+00 4.00e-02 2.26e+02 dihedral pdb=" CA PRO B 482 " pdb=" C PRO B 482 " pdb=" N ASN B 483 " pdb=" CA ASN B 483 " ideal model delta harmonic sigma weight residual 180.00 145.34 34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA VAL B 366 " pdb=" C VAL B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual -180.00 -149.82 -30.18 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 21346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5350 0.128 - 0.257: 373 0.257 - 0.385: 44 0.385 - 0.513: 5 0.513 - 0.641: 2 Chirality restraints: 5774 Sorted by residual: chirality pdb=" CA SERb1 130 " pdb=" N SERb1 130 " pdb=" C SERb1 130 " pdb=" CB SERb1 130 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA GLUb2 67 " pdb=" N GLUb2 67 " pdb=" C GLUb2 67 " pdb=" CB GLUb2 67 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA LYSb1 60 " pdb=" N LYSb1 60 " pdb=" C LYSb1 60 " pdb=" CB LYSb1 60 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 5771 not shown) Planarity restraints: 6223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 189 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO G 190 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO G 190 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO G 190 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEUb1 68 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C LEUb1 68 " 0.057 2.00e-02 2.50e+03 pdb=" O LEUb1 68 " -0.021 2.00e-02 2.50e+03 pdb=" N METb1 69 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAb2 58 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ALAb2 58 " -0.056 2.00e-02 2.50e+03 pdb=" O ALAb2 58 " 0.022 2.00e-02 2.50e+03 pdb=" N GLUb2 59 " 0.017 2.00e-02 2.50e+03 ... (remaining 6220 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.45: 5 1.45 - 2.31: 68 2.31 - 3.18: 29739 3.18 - 4.04: 91891 4.04 - 4.90: 169179 Warning: very small nonbonded interaction distances. Nonbonded interactions: 290882 Sorted by model distance: nonbonded pdb=" C ALAc3 35 " pdb=" OE2 GLU H 31 " model vdw 0.590 3.270 nonbonded pdb=" O ALAc3 35 " pdb=" OE2 GLU H 31 " model vdw 0.858 3.040 nonbonded pdb=" C ARGc3 36 " pdb=" OE1 GLU H 31 " model vdw 0.901 3.270 nonbonded pdb=" O ARGc3 36 " pdb=" OE1 GLU H 31 " model vdw 1.223 3.040 nonbonded pdb=" O ALAc3 35 " pdb=" CD GLU H 31 " model vdw 1.242 3.270 ... (remaining 290877 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 20 and (name N or name CA or name C or name O o \ r 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 392 or (resid 393 and (name \ N or name CA or name C or name O or name CB )) or (resid 394 and (name N or name \ CA or name C or name CB )) or resid 395 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 466 through 501 or resid 60 \ 0 through 601)) selection = (chain 'B' and ((resid 8 through 20 and (name N or name CA or name C or name O o \ r name CB )) or resid 21 through 22 or (resid 23 through 24 and (name N or name \ CA or name C or name O or name CB )) or resid 25 through 38 or (resid 39 and (na \ me N or name CA or name C or name CB )) or resid 40 through 352 or (resid 353 an \ d (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 354 \ through 392 or (resid 393 and (name N or name CA or name C or name O or name CB \ )) or (resid 394 and (name N or name CA or name C or name CB )) or resid 395 th \ rough 396 or (resid 397 through 398 and (name N or name CA or name C or name O o \ r name CB )) or resid 399 through 402 or (resid 403 through 406 and (name N or n \ ame CA or name C or name O or name CB )) or resid 407 through 450 or (resid 451 \ and (name N or name CA or name C or name O or name CB )) or resid 452 through 48 \ 4 or (resid 485 and (name N or name CA or name C or name O or name CB )) or resi \ d 486 through 488 or (resid 489 through 490 and (name N or name CA or name C or \ name O or name CB )) or resid 491 through 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 throu \ gh 601)) selection = (chain 'C' and (resid 8 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 187 or (resid 188 and (n \ ame N or name CA or name C or name O or name CB )) or resid 189 through 352 or ( \ resid 353 and (name N or name CA or name C or name CB or name CG1 or name CG2)) \ or resid 354 through 396 or (resid 397 through 398 and (name N or name CA or nam \ e C or name O or name CB )) or resid 399 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 450 or (resid 4 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 452 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or r \ esid 466 through 484 or (resid 485 and (name N or name CA or name C or name O or \ name CB )) or resid 486 through 488 or (resid 489 through 490 and (name N or na \ me CA or name C or name O or name CB )) or resid 491 through 495 or (resid 496 a \ nd (name N or name CA or name C or name O or name CB )) or resid 497 through 501 \ or resid 600 through 601)) } ncs_group { reference = (chain 'D' 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 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 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 resid 423 through 469)) selection = (chain 'E' 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 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 381 or (resid 38 \ 2 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 and (name N or name CA or name C or name O or name \ CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name C o \ r name O or name CB )) or resid 396 or (resid 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 or name O or name CB )) or resid 432 through 468 or (resid 46 \ 9 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 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 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or re \ sid 398 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 468 or (resid 469 and (name N or name CA or name C or name O or n \ ame CB )))) } 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 139 and \ (name N or name CA or name C or name O or name CB )) or (resid 140 and (name N o \ r name CA or name C 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.990 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 87.450 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.011 0.127 35388 Z= 0.715 Angle : 1.268 20.760 48101 Z= 0.776 Chirality : 0.075 0.641 5774 Planarity : 0.008 0.108 6223 Dihedral : 10.944 87.122 12769 Min Nonbonded Distance : 0.590 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 0.78 % Allowed : 5.83 % Favored : 93.39 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.11), residues: 4646 helix: -1.52 (0.09), residues: 2495 sheet: -1.55 (0.21), residues: 546 loop : -2.02 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 206 HIS 0.031 0.003 HIS D 363 PHE 0.043 0.004 PHEc9 65 TYR 0.035 0.003 TYRc3 69 ARG 0.010 0.001 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 691 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 184 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4978 (mt) REVERT: a 223 MET cc_start: 0.7704 (tmm) cc_final: 0.7482 (tmm) REVERT: C 354 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8021 (mtt90) REVERT: C 363 VAL cc_start: 0.8420 (p) cc_final: 0.8087 (m) REVERT: C 458 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7537 (tttm) REVERT: C 489 LYS cc_start: 0.8307 (mmtm) cc_final: 0.8031 (mmtm) REVERT: A 54 GLU cc_start: 0.7853 (tt0) cc_final: 0.7623 (tt0) REVERT: A 326 ILE cc_start: 0.9014 (tt) cc_final: 0.8745 (tt) REVERT: A 363 VAL cc_start: 0.8664 (t) cc_final: 0.8393 (m) REVERT: A 393 GLU cc_start: 0.7212 (pp20) cc_final: 0.6965 (pp20) REVERT: A 436 ILE cc_start: 0.7954 (mm) cc_final: 0.7697 (tp) REVERT: A 458 LYS cc_start: 0.7989 (ttpm) cc_final: 0.7761 (ttpt) REVERT: A 463 PHE cc_start: 0.8590 (t80) cc_final: 0.8191 (t80) REVERT: B 60 MET cc_start: 0.8898 (mmt) cc_final: 0.8254 (mmt) REVERT: B 129 ILE cc_start: 0.9151 (tt) cc_final: 0.8921 (tt) REVERT: B 157 VAL cc_start: 0.9254 (t) cc_final: 0.9003 (t) REVERT: B 262 ASP cc_start: 0.8238 (m-30) cc_final: 0.8014 (m-30) REVERT: B 289 ASP cc_start: 0.8766 (p0) cc_final: 0.8492 (p0) REVERT: B 384 LEU cc_start: 0.8311 (mt) cc_final: 0.8101 (mt) REVERT: B 440 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8839 (tp) REVERT: B 489 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8170 (ttmm) REVERT: F 10 MET cc_start: 0.7401 (mtp) cc_final: 0.7128 (mtm) REVERT: F 17 LYS cc_start: 0.8462 (tttt) cc_final: 0.8081 (ttmt) REVERT: F 74 MET cc_start: 0.8747 (mtt) cc_final: 0.8509 (mtt) REVERT: F 307 TYR cc_start: 0.7763 (t80) cc_final: 0.7555 (t80) REVERT: F 375 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8132 (tp40) REVERT: F 381 GLN cc_start: 0.8116 (tt0) cc_final: 0.7757 (tp-100) REVERT: D 44 ILE cc_start: 0.8392 (mt) cc_final: 0.8155 (tp) REVERT: D 62 ILE cc_start: 0.8897 (tp) cc_final: 0.8572 (pt) REVERT: D 143 ASP cc_start: 0.8255 (m-30) cc_final: 0.7579 (m-30) REVERT: D 168 ILE cc_start: 0.8627 (mt) cc_final: 0.8348 (mm) REVERT: D 175 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.7767 (mp) REVERT: D 420 PHE cc_start: 0.8950 (m-10) cc_final: 0.8745 (m-10) REVERT: E 7 ILE cc_start: 0.9149 (mt) cc_final: 0.8928 (mm) REVERT: E 39 GLU cc_start: 0.7811 (pm20) cc_final: 0.7549 (pm20) REVERT: E 454 ARG cc_start: 0.8857 (mtt-85) cc_final: 0.8448 (mtt-85) REVERT: G 84 ASP cc_start: 0.8018 (t0) cc_final: 0.7689 (t0) REVERT: G 120 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7416 (mtm-85) REVERT: G 168 LEU cc_start: 0.7991 (pt) cc_final: 0.7742 (pt) REVERT: G 204 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7162 (tm-30) REVERT: H 112 ASP cc_start: 0.7670 (m-30) cc_final: 0.7276 (m-30) REVERT: I 3 GLN cc_start: 0.7307 (tm-30) cc_final: 0.6892 (tm-30) REVERT: I 57 GLN cc_start: 0.8685 (mm110) cc_final: 0.8419 (mm-40) REVERT: I 69 VAL cc_start: 0.8368 (m) cc_final: 0.8030 (t) REVERT: I 88 LEU cc_start: 0.7772 (tt) cc_final: 0.7023 (mm) REVERT: I 110 VAL cc_start: 0.8268 (t) cc_final: 0.8058 (p) REVERT: I 175 GLN cc_start: 0.7991 (tt0) cc_final: 0.7720 (tt0) outliers start: 27 outliers final: 9 residues processed: 714 average time/residue: 0.4916 time to fit residues: 553.5477 Evaluate side-chains 492 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 480 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 0.0470 chunk 352 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 364 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 271 optimal weight: 0.6980 chunk 422 optimal weight: 5.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN a 128 HIS ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 HIS ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 37 GLN c8 23 ASN c0 23 ASN c0 37 GLN C 186 GLN C 422 GLN C 425 HIS A 186 GLN A 322 GLN A 422 GLN A 425 HIS ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 215 HIS F 169 GLN F 179 HIS F 217 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 289 GLN D 304 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN E 304 GLN E 324 HIS G 55 ASN G 174 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 35388 Z= 0.207 Angle : 0.662 15.523 48101 Z= 0.335 Chirality : 0.045 0.215 5774 Planarity : 0.006 0.090 6223 Dihedral : 6.986 88.505 5183 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 2.58 % Allowed : 10.32 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4646 helix: -0.12 (0.10), residues: 2506 sheet: -1.27 (0.21), residues: 543 loop : -1.43 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 206 HIS 0.009 0.001 HIS E 363 PHE 0.031 0.002 PHE a 87 TYR 0.041 0.002 TYRc9 69 ARG 0.009 0.000 ARGb2 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 529 time to evaluate : 3.676 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 E 421 " (corrupted residue). Skipping it. REVERT: b1 36 ILE cc_start: 0.8084 (mp) cc_final: 0.7881 (mp) REVERT: a 22 MET cc_start: 0.5492 (mmm) cc_final: 0.5255 (mmm) REVERT: a 122 MET cc_start: 0.6125 (tmm) cc_final: 0.5588 (tmm) REVERT: a 223 MET cc_start: 0.7800 (tmm) cc_final: 0.7506 (tmm) REVERT: C 363 VAL cc_start: 0.8417 (p) cc_final: 0.8087 (m) REVERT: C 402 LEU cc_start: 0.6638 (mp) cc_final: 0.6291 (tp) REVERT: C 452 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7420 (t70) REVERT: C 458 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7454 (tttm) REVERT: C 489 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8075 (mmtm) REVERT: A 54 GLU cc_start: 0.8179 (tt0) cc_final: 0.7908 (tt0) REVERT: A 89 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7815 (mtp-110) REVERT: A 125 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 273 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9032 (tm) REVERT: A 463 PHE cc_start: 0.8290 (t80) cc_final: 0.8039 (t80) REVERT: B 96 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 129 ILE cc_start: 0.9164 (tt) cc_final: 0.8942 (tt) REVERT: B 289 ASP cc_start: 0.8805 (p0) cc_final: 0.8515 (p0) REVERT: F 17 LYS cc_start: 0.8409 (tttt) cc_final: 0.7991 (ttmt) REVERT: F 42 VAL cc_start: 0.8054 (t) cc_final: 0.7720 (m) REVERT: F 273 SER cc_start: 0.8765 (t) cc_final: 0.8430 (t) REVERT: F 375 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8010 (tp40) REVERT: F 381 GLN cc_start: 0.8059 (tt0) cc_final: 0.7746 (tp-100) REVERT: D 10 MET cc_start: 0.7849 (mtp) cc_final: 0.7538 (mtm) REVERT: D 44 ILE cc_start: 0.8229 (mt) cc_final: 0.7959 (tp) REVERT: D 143 ASP cc_start: 0.8125 (m-30) cc_final: 0.7657 (m-30) REVERT: D 144 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8184 (tm) REVERT: D 168 ILE cc_start: 0.8475 (mt) cc_final: 0.8249 (mm) REVERT: D 364 TYR cc_start: 0.8655 (t80) cc_final: 0.8344 (t80) REVERT: D 378 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8343 (tppt) REVERT: E 5 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7534 (mmm160) REVERT: E 39 GLU cc_start: 0.7726 (pm20) cc_final: 0.7485 (pm20) REVERT: E 454 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8465 (mtt-85) REVERT: G 84 ASP cc_start: 0.7982 (t0) cc_final: 0.7545 (t0) REVERT: G 120 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7192 (mtm-85) REVERT: G 127 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7252 (mtt-85) REVERT: G 204 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7066 (tm-30) REVERT: H 4 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5115 (pp) REVERT: H 32 LEU cc_start: 0.8195 (tt) cc_final: 0.7929 (tt) REVERT: I 57 GLN cc_start: 0.8722 (mm110) cc_final: 0.8458 (mm-40) REVERT: I 69 VAL cc_start: 0.8014 (m) cc_final: 0.7282 (m) REVERT: I 88 LEU cc_start: 0.7742 (tt) cc_final: 0.7131 (mm) REVERT: I 110 VAL cc_start: 0.8016 (t) cc_final: 0.7602 (p) REVERT: I 175 GLN cc_start: 0.7927 (tt0) cc_final: 0.7678 (tt0) outliers start: 89 outliers final: 34 residues processed: 594 average time/residue: 0.4470 time to fit residues: 436.4954 Evaluate side-chains 495 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 457 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 351 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 423 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 chunk 419 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 433 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 35388 Z= 0.331 Angle : 0.686 16.275 48101 Z= 0.339 Chirality : 0.047 0.287 5774 Planarity : 0.005 0.084 6223 Dihedral : 6.769 86.856 5172 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 3.71 % Allowed : 11.54 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.63 (0.12), residues: 4646 helix: 0.35 (0.10), residues: 2496 sheet: -1.14 (0.21), residues: 552 loop : -1.23 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP a 206 HIS 0.009 0.001 HIS E 363 PHE 0.033 0.002 PHE a 87 TYR 0.028 0.002 TYRc9 69 ARG 0.006 0.000 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 469 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b1 36 ILE cc_start: 0.8051 (mp) cc_final: 0.7847 (mp) REVERT: a 223 MET cc_start: 0.7710 (tmm) cc_final: 0.7420 (tmm) REVERT: C 129 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.7684 (mt) REVERT: C 402 LEU cc_start: 0.6589 (mp) cc_final: 0.6251 (tp) REVERT: C 407 GLN cc_start: 0.7163 (mt0) cc_final: 0.6950 (mt0) REVERT: C 452 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7506 (t70) REVERT: C 458 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7544 (tttm) REVERT: C 489 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8069 (mmtm) REVERT: A 54 GLU cc_start: 0.8167 (tt0) cc_final: 0.7593 (tt0) REVERT: A 125 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 250 MET cc_start: 0.8993 (ttp) cc_final: 0.8735 (ttt) REVERT: A 326 ILE cc_start: 0.9077 (tt) cc_final: 0.8772 (tt) REVERT: A 463 PHE cc_start: 0.8273 (t80) cc_final: 0.7957 (t80) REVERT: A 466 GLN cc_start: 0.7826 (pp30) cc_final: 0.7545 (pp30) REVERT: B 60 MET cc_start: 0.8929 (mmt) cc_final: 0.8665 (mmt) REVERT: B 262 ASP cc_start: 0.8208 (m-30) cc_final: 0.7931 (m-30) REVERT: B 289 ASP cc_start: 0.8882 (p0) cc_final: 0.8590 (p0) REVERT: B 489 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8156 (ttmm) REVERT: F 17 LYS cc_start: 0.8507 (tttt) cc_final: 0.8069 (ttmt) REVERT: F 77 ILE cc_start: 0.8720 (mt) cc_final: 0.8495 (mp) REVERT: F 285 MET cc_start: 0.8983 (tpp) cc_final: 0.8780 (tpp) REVERT: F 381 GLN cc_start: 0.8059 (tt0) cc_final: 0.7727 (tp-100) REVERT: D 10 MET cc_start: 0.7943 (mtp) cc_final: 0.7627 (mtm) REVERT: D 44 ILE cc_start: 0.8325 (mt) cc_final: 0.8080 (tp) REVERT: D 144 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (tm) REVERT: D 364 TYR cc_start: 0.8749 (t80) cc_final: 0.8481 (t80) REVERT: D 378 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8372 (tppt) REVERT: E 39 GLU cc_start: 0.7709 (pm20) cc_final: 0.7493 (pm20) REVERT: E 170 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: E 233 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (tp) REVERT: E 334 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8098 (ptmm) REVERT: G 22 LYS cc_start: 0.8045 (tttp) cc_final: 0.7778 (tppt) REVERT: G 84 ASP cc_start: 0.8026 (t0) cc_final: 0.7628 (t0) REVERT: G 120 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7188 (mtm-85) REVERT: G 127 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7239 (mtt-85) REVERT: G 204 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7080 (tm-30) REVERT: H 4 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5555 (pp) REVERT: H 32 LEU cc_start: 0.8182 (tt) cc_final: 0.7880 (tt) REVERT: I 57 GLN cc_start: 0.8752 (mm110) cc_final: 0.8525 (mm-40) REVERT: I 69 VAL cc_start: 0.8177 (m) cc_final: 0.7941 (m) REVERT: I 88 LEU cc_start: 0.7901 (tt) cc_final: 0.7408 (mm) REVERT: I 110 VAL cc_start: 0.7971 (t) cc_final: 0.7530 (p) outliers start: 128 outliers final: 68 residues processed: 559 average time/residue: 0.4505 time to fit residues: 414.7315 Evaluate side-chains 524 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 450 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 0.4980 chunk 318 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 424 optimal weight: 0.3980 chunk 449 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 402 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c0 37 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 304 GLN G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35388 Z= 0.291 Angle : 0.679 26.794 48101 Z= 0.328 Chirality : 0.046 0.287 5774 Planarity : 0.005 0.079 6223 Dihedral : 6.590 87.680 5172 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 3.77 % Allowed : 13.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 4646 helix: 0.63 (0.10), residues: 2496 sheet: -1.02 (0.21), residues: 534 loop : -1.10 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 206 HIS 0.008 0.001 HIS E 363 PHE 0.032 0.001 PHE a 87 TYR 0.023 0.001 TYRc9 69 ARG 0.009 0.000 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 457 time to evaluate : 4.105 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 E 421 " (corrupted residue). Skipping it. REVERT: a 223 MET cc_start: 0.7683 (tmm) cc_final: 0.7462 (tmm) REVERT: C 129 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.7769 (mt) REVERT: C 402 LEU cc_start: 0.6578 (mp) cc_final: 0.6181 (tp) REVERT: C 407 GLN cc_start: 0.7279 (mt0) cc_final: 0.7058 (mt0) REVERT: C 452 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7614 (t70) REVERT: C 458 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7474 (tttm) REVERT: C 489 LYS cc_start: 0.8302 (mmtm) cc_final: 0.8071 (mmtm) REVERT: A 125 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 165 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: A 250 MET cc_start: 0.8964 (ttp) cc_final: 0.8699 (ttt) REVERT: A 326 ILE cc_start: 0.9089 (tt) cc_final: 0.8782 (tt) REVERT: B 60 MET cc_start: 0.8894 (mmt) cc_final: 0.8650 (mmt) REVERT: B 262 ASP cc_start: 0.8175 (m-30) cc_final: 0.7900 (m-30) REVERT: B 289 ASP cc_start: 0.8877 (p0) cc_final: 0.8625 (p0) REVERT: B 489 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8146 (ttmm) REVERT: F 17 LYS cc_start: 0.8534 (tttt) cc_final: 0.8077 (ttmt) REVERT: F 77 ILE cc_start: 0.8796 (mt) cc_final: 0.8576 (mp) REVERT: F 381 GLN cc_start: 0.7974 (tt0) cc_final: 0.7676 (tp-100) REVERT: D 10 MET cc_start: 0.7957 (mtp) cc_final: 0.7614 (mtm) REVERT: D 44 ILE cc_start: 0.8330 (mt) cc_final: 0.8123 (tp) REVERT: D 144 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8241 (tm) REVERT: D 364 TYR cc_start: 0.8756 (t80) cc_final: 0.8489 (t80) REVERT: D 378 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8378 (tppt) REVERT: E 39 GLU cc_start: 0.7704 (pm20) cc_final: 0.7495 (pm20) REVERT: E 177 GLN cc_start: 0.7944 (mt0) cc_final: 0.7432 (mp10) REVERT: E 233 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (tp) REVERT: E 288 LEU cc_start: 0.9165 (tp) cc_final: 0.8961 (tp) REVERT: E 334 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8065 (ptmm) REVERT: G 22 LYS cc_start: 0.8068 (tttp) cc_final: 0.7784 (tppt) REVERT: G 84 ASP cc_start: 0.7965 (t0) cc_final: 0.7642 (t0) REVERT: G 120 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.7076 (mtm-85) REVERT: G 127 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7278 (mtt-85) REVERT: G 204 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7051 (tm-30) REVERT: H 4 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5664 (pp) REVERT: H 32 LEU cc_start: 0.7890 (tt) cc_final: 0.7599 (tt) REVERT: I 88 LEU cc_start: 0.7824 (tt) cc_final: 0.7329 (mm) outliers start: 130 outliers final: 80 residues processed: 553 average time/residue: 0.4395 time to fit residues: 401.4677 Evaluate side-chains 527 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 441 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 6 optimal weight: 30.0000 chunk 334 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 383 optimal weight: 0.5980 chunk 310 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 229 optimal weight: 1.9990 chunk 403 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35388 Z= 0.336 Angle : 0.684 19.012 48101 Z= 0.334 Chirality : 0.048 0.481 5774 Planarity : 0.005 0.078 6223 Dihedral : 6.522 88.670 5172 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 4.03 % Allowed : 14.12 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.18 (0.12), residues: 4646 helix: 0.73 (0.10), residues: 2496 sheet: -1.03 (0.21), residues: 548 loop : -1.01 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 206 HIS 0.008 0.001 HIS E 363 PHE 0.029 0.001 PHE a 87 TYR 0.034 0.002 TYRb2 13 ARG 0.011 0.000 ARGb1 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 454 time to evaluate : 4.201 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 E 421 " (corrupted residue). Skipping it. REVERT: b2 26 ARG cc_start: 0.7163 (ptm-80) cc_final: 0.6560 (ptm-80) REVERT: C 129 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.7814 (mt) REVERT: C 347 ASP cc_start: 0.8352 (t0) cc_final: 0.8106 (t0) REVERT: C 402 LEU cc_start: 0.6526 (mp) cc_final: 0.6105 (tp) REVERT: C 407 GLN cc_start: 0.7131 (mt0) cc_final: 0.6883 (mt0) REVERT: C 415 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7254 (mtt-85) REVERT: C 458 LYS cc_start: 0.7741 (ttpp) cc_final: 0.7465 (tttm) REVERT: C 489 LYS cc_start: 0.8318 (mmtm) cc_final: 0.8082 (mmtm) REVERT: A 125 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 165 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: A 250 MET cc_start: 0.8989 (ttp) cc_final: 0.8740 (ttt) REVERT: A 326 ILE cc_start: 0.9088 (tt) cc_final: 0.8815 (tt) REVERT: B 60 MET cc_start: 0.8889 (mmt) cc_final: 0.8641 (mmt) REVERT: B 262 ASP cc_start: 0.8404 (m-30) cc_final: 0.8152 (m-30) REVERT: B 289 ASP cc_start: 0.8915 (p0) cc_final: 0.8712 (p0) REVERT: B 489 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8183 (ttmm) REVERT: F 17 LYS cc_start: 0.8555 (tttt) cc_final: 0.8097 (ttmt) REVERT: F 381 GLN cc_start: 0.7977 (tt0) cc_final: 0.7722 (tp40) REVERT: D 10 MET cc_start: 0.8003 (mtp) cc_final: 0.7641 (mtm) REVERT: D 144 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8249 (tm) REVERT: D 364 TYR cc_start: 0.8792 (t80) cc_final: 0.8499 (t80) REVERT: D 378 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8371 (tppt) REVERT: E 39 GLU cc_start: 0.7682 (pm20) cc_final: 0.7474 (pm20) REVERT: E 124 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7912 (mmtt) REVERT: E 170 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6217 (tt0) REVERT: E 177 GLN cc_start: 0.7949 (mt0) cc_final: 0.7442 (mp10) REVERT: E 233 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8186 (tp) REVERT: E 361 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6671 (mp0) REVERT: G 22 LYS cc_start: 0.8106 (tttp) cc_final: 0.7803 (tppt) REVERT: G 84 ASP cc_start: 0.7885 (t0) cc_final: 0.7599 (t0) REVERT: G 120 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.6979 (mtm-85) REVERT: G 127 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7338 (ttm-80) REVERT: G 139 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7658 (tpp80) REVERT: G 204 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7044 (tm-30) REVERT: H 4 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.5743 (pp) REVERT: H 32 LEU cc_start: 0.7904 (tt) cc_final: 0.7615 (tt) REVERT: I 88 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7397 (mm) outliers start: 139 outliers final: 91 residues processed: 556 average time/residue: 0.4448 time to fit residues: 405.5695 Evaluate side-chains 538 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 439 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c0 residue 43 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 0.9980 chunk 404 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 217 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35388 Z= 0.238 Angle : 0.664 23.421 48101 Z= 0.318 Chirality : 0.046 0.453 5774 Planarity : 0.004 0.076 6223 Dihedral : 6.339 87.932 5172 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 3.60 % Allowed : 15.28 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.03 (0.12), residues: 4646 helix: 0.89 (0.10), residues: 2497 sheet: -0.99 (0.21), residues: 533 loop : -0.87 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 206 HIS 0.007 0.001 HIS E 363 PHE 0.026 0.001 PHE a 87 TYR 0.021 0.001 TYR D 377 ARG 0.008 0.000 ARG D 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 454 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: C 129 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 130 GLU cc_start: 0.8301 (tp30) cc_final: 0.8052 (tp30) REVERT: C 347 ASP cc_start: 0.8351 (t0) cc_final: 0.8126 (t0) REVERT: C 402 LEU cc_start: 0.6612 (mp) cc_final: 0.6176 (tp) REVERT: C 407 GLN cc_start: 0.7058 (mt0) cc_final: 0.6815 (mt0) REVERT: C 415 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: C 452 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7686 (t70) REVERT: C 458 LYS cc_start: 0.7743 (ttpp) cc_final: 0.7511 (tttm) REVERT: C 489 LYS cc_start: 0.8309 (mmtm) cc_final: 0.8075 (mmtm) REVERT: A 165 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: A 250 MET cc_start: 0.8973 (ttp) cc_final: 0.8733 (ttt) REVERT: A 326 ILE cc_start: 0.9089 (tt) cc_final: 0.8818 (tt) REVERT: A 393 GLU cc_start: 0.7508 (pp20) cc_final: 0.7239 (pp20) REVERT: B 489 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8158 (ttmm) REVERT: F 17 LYS cc_start: 0.8583 (tttt) cc_final: 0.8126 (ttmt) REVERT: F 381 GLN cc_start: 0.7950 (tt0) cc_final: 0.7712 (tp40) REVERT: D 10 MET cc_start: 0.7955 (mtp) cc_final: 0.7598 (mtm) REVERT: D 144 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8187 (tm) REVERT: D 364 TYR cc_start: 0.8748 (t80) cc_final: 0.8455 (t80) REVERT: D 378 LYS cc_start: 0.8631 (ttpp) cc_final: 0.8361 (tppt) REVERT: E 39 GLU cc_start: 0.7667 (pm20) cc_final: 0.7458 (pm20) REVERT: E 170 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: E 177 GLN cc_start: 0.7959 (mt0) cc_final: 0.7435 (mp10) REVERT: G 22 LYS cc_start: 0.8075 (tttp) cc_final: 0.7782 (tppt) REVERT: G 120 ARG cc_start: 0.7542 (ttp-110) cc_final: 0.6938 (mtm-85) REVERT: G 127 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7313 (ttm-80) REVERT: G 139 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7665 (tpp80) REVERT: G 170 MET cc_start: 0.8083 (ttm) cc_final: 0.7882 (ttm) REVERT: G 204 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7002 (tm-30) REVERT: H 4 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6002 (pp) REVERT: H 32 LEU cc_start: 0.7890 (tt) cc_final: 0.7582 (tt) REVERT: I 88 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7423 (mm) outliers start: 124 outliers final: 88 residues processed: 549 average time/residue: 0.4773 time to fit residues: 434.6518 Evaluate side-chains 525 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 429 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c3 residue 70 LEU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 58 LEU Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c0 residue 43 VAL Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 378 optimal weight: 0.9980 chunk 251 optimal weight: 0.4980 chunk 448 optimal weight: 0.9990 chunk 280 optimal weight: 0.0170 chunk 273 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN F 33 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 217 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35388 Z= 0.192 Angle : 0.638 19.064 48101 Z= 0.306 Chirality : 0.045 0.423 5774 Planarity : 0.004 0.075 6223 Dihedral : 6.134 85.652 5172 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 3.19 % Allowed : 16.12 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.24 (0.12), residues: 4646 helix: 1.04 (0.10), residues: 2499 sheet: -0.88 (0.21), residues: 514 loop : -0.75 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 206 HIS 0.006 0.001 HIS E 363 PHE 0.022 0.001 PHE a 221 TYR 0.015 0.001 TYR D 377 ARG 0.013 0.000 ARGb1 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 460 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 129 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.7691 (mt) REVERT: C 347 ASP cc_start: 0.8338 (t0) cc_final: 0.8102 (t0) REVERT: C 402 LEU cc_start: 0.6522 (mp) cc_final: 0.6083 (tp) REVERT: C 407 GLN cc_start: 0.6985 (mt0) cc_final: 0.6726 (mt0) REVERT: C 415 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7139 (mtt-85) REVERT: C 452 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7668 (t70) REVERT: A 15 GLN cc_start: 0.8487 (mt0) cc_final: 0.8215 (mt0) REVERT: A 165 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 326 ILE cc_start: 0.9103 (tt) cc_final: 0.8826 (tt) REVERT: B 489 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8171 (ttmm) REVERT: F 17 LYS cc_start: 0.8514 (tttt) cc_final: 0.8060 (ttmt) REVERT: F 381 GLN cc_start: 0.7963 (tt0) cc_final: 0.7722 (tp40) REVERT: D 10 MET cc_start: 0.7913 (mtp) cc_final: 0.7566 (mtm) REVERT: D 144 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8172 (tm) REVERT: D 364 TYR cc_start: 0.8712 (t80) cc_final: 0.8477 (t80) REVERT: D 378 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8319 (tppt) REVERT: E 39 GLU cc_start: 0.7670 (pm20) cc_final: 0.7445 (pm20) REVERT: E 170 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: E 177 GLN cc_start: 0.8017 (mt0) cc_final: 0.7524 (mp10) REVERT: E 334 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7849 (ptmm) REVERT: G 127 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7298 (ttm-80) REVERT: G 204 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6947 (tm-30) REVERT: H 4 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6226 (pp) REVERT: H 32 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7563 (tt) REVERT: I 88 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7357 (mm) outliers start: 110 outliers final: 76 residues processed: 538 average time/residue: 0.4541 time to fit residues: 401.3831 Evaluate side-chains 521 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 436 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c3 residue 70 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c0 residue 43 VAL Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 0.0370 chunk 178 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 284 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN A 163 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN F 33 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 259 GLN ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35388 Z= 0.195 Angle : 0.650 18.971 48101 Z= 0.309 Chirality : 0.045 0.376 5774 Planarity : 0.004 0.075 6223 Dihedral : 5.983 83.592 5168 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 3.10 % Allowed : 16.41 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 4646 helix: 1.15 (0.10), residues: 2493 sheet: -0.79 (0.22), residues: 514 loop : -0.70 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 206 HIS 0.006 0.001 HIS E 363 PHE 0.025 0.001 PHE a 160 TYR 0.014 0.001 TYR D 377 ARG 0.020 0.000 ARGb1 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 459 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: C 129 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 347 ASP cc_start: 0.8324 (t0) cc_final: 0.8104 (t0) REVERT: C 402 LEU cc_start: 0.6515 (mp) cc_final: 0.6076 (tp) REVERT: C 407 GLN cc_start: 0.6980 (mt0) cc_final: 0.6710 (mt0) REVERT: C 415 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7142 (mtt-85) REVERT: C 452 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7846 (t70) REVERT: C 462 LEU cc_start: 0.7831 (mm) cc_final: 0.7616 (mp) REVERT: A 165 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: A 250 MET cc_start: 0.8950 (ttt) cc_final: 0.8745 (ttt) REVERT: A 326 ILE cc_start: 0.9105 (tt) cc_final: 0.8825 (tt) REVERT: B 489 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8184 (ttmm) REVERT: F 17 LYS cc_start: 0.8515 (tttt) cc_final: 0.8061 (ttmt) REVERT: F 381 GLN cc_start: 0.7972 (tt0) cc_final: 0.7714 (tp40) REVERT: F 389 MET cc_start: 0.8856 (tpt) cc_final: 0.8611 (tpp) REVERT: D 10 MET cc_start: 0.7922 (mtp) cc_final: 0.7571 (mtm) REVERT: D 144 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (tm) REVERT: D 364 TYR cc_start: 0.8694 (t80) cc_final: 0.8469 (t80) REVERT: D 378 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8317 (tppt) REVERT: E 39 GLU cc_start: 0.7636 (pm20) cc_final: 0.7411 (pm20) REVERT: E 170 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6073 (tt0) REVERT: E 177 GLN cc_start: 0.8037 (mt0) cc_final: 0.7546 (mp10) REVERT: E 334 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7866 (ptmm) REVERT: G 127 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7310 (ttm-80) REVERT: G 204 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6932 (tm-30) REVERT: H 4 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6278 (pp) REVERT: H 32 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7592 (tt) REVERT: I 3 GLN cc_start: 0.6859 (tm-30) cc_final: 0.6617 (tm-30) REVERT: I 88 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7299 (mm) outliers start: 107 outliers final: 82 residues processed: 537 average time/residue: 0.4677 time to fit residues: 416.7563 Evaluate side-chains 529 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 438 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c3 residue 70 LEU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c0 residue 43 VAL Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 0.7980 chunk 429 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 417 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 327 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 377 optimal weight: 0.9980 chunk 395 optimal weight: 0.7980 chunk 416 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35388 Z= 0.199 Angle : 0.659 21.021 48101 Z= 0.312 Chirality : 0.045 0.372 5774 Planarity : 0.004 0.074 6223 Dihedral : 5.930 81.835 5168 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 2.81 % Allowed : 17.14 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.45 (0.12), residues: 4646 helix: 1.23 (0.11), residues: 2475 sheet: -0.77 (0.22), residues: 517 loop : -0.68 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRPb2 30 HIS 0.006 0.001 HIS E 363 PHE 0.024 0.001 PHE a 87 TYR 0.014 0.001 TYR D 377 ARG 0.014 0.000 ARGb1 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 459 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: C 129 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.7637 (mt) REVERT: C 347 ASP cc_start: 0.8332 (t0) cc_final: 0.8125 (t0) REVERT: C 402 LEU cc_start: 0.6448 (mp) cc_final: 0.6041 (tp) REVERT: C 407 GLN cc_start: 0.6985 (mt0) cc_final: 0.6707 (mt0) REVERT: C 415 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7139 (mtt-85) REVERT: C 452 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7858 (t70) REVERT: C 462 LEU cc_start: 0.7863 (mm) cc_final: 0.7644 (mp) REVERT: A 165 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 250 MET cc_start: 0.8961 (ttt) cc_final: 0.8751 (ttt) REVERT: A 326 ILE cc_start: 0.9107 (tt) cc_final: 0.8825 (tt) REVERT: B 489 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8219 (ttmm) REVERT: F 17 LYS cc_start: 0.8514 (tttt) cc_final: 0.8059 (ttmt) REVERT: F 381 GLN cc_start: 0.7965 (tt0) cc_final: 0.7712 (tp40) REVERT: F 389 MET cc_start: 0.8822 (tpt) cc_final: 0.8614 (tpp) REVERT: D 10 MET cc_start: 0.7915 (mtp) cc_final: 0.7569 (mtm) REVERT: D 144 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8157 (tm) REVERT: D 364 TYR cc_start: 0.8678 (t80) cc_final: 0.8462 (t80) REVERT: D 378 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8319 (tppt) REVERT: E 3 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7406 (mtt-85) REVERT: E 39 GLU cc_start: 0.7621 (pm20) cc_final: 0.7419 (pm20) REVERT: E 170 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6053 (tt0) REVERT: E 177 GLN cc_start: 0.8042 (mt0) cc_final: 0.7550 (mp10) REVERT: E 334 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7873 (ptmm) REVERT: G 120 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7273 (mtm110) REVERT: G 127 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7297 (ttm-80) REVERT: G 204 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6729 (tm-30) REVERT: H 4 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6253 (pp) REVERT: H 32 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7604 (tt) REVERT: I 88 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7418 (mm) outliers start: 97 outliers final: 80 residues processed: 528 average time/residue: 0.4417 time to fit residues: 384.4627 Evaluate side-chains 534 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 445 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 25 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c3 residue 70 LEU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 0.0570 chunk 441 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 307 optimal weight: 0.3980 chunk 463 optimal weight: 9.9990 chunk 426 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 37 GLN C 433 GLN A 15 GLN A 163 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35388 Z= 0.221 Angle : 0.667 21.150 48101 Z= 0.316 Chirality : 0.045 0.382 5774 Planarity : 0.004 0.074 6223 Dihedral : 5.915 80.430 5167 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 2.81 % Allowed : 17.37 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 4646 helix: 1.20 (0.10), residues: 2509 sheet: -0.69 (0.22), residues: 522 loop : -0.66 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPb2 30 HIS 0.006 0.001 HIS E 363 PHE 0.021 0.001 PHE a 87 TYR 0.015 0.001 TYR D 377 ARG 0.014 0.000 ARGb1 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9292 Ramachandran restraints generated. 4646 Oldfield, 0 Emsley, 4646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 458 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR E 421 " (corrupted residue). Skipping it. REVERT: b2 27 LYS cc_start: 0.6889 (mmtm) cc_final: 0.6200 (mmtp) REVERT: C 129 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.7633 (mt) REVERT: C 402 LEU cc_start: 0.6445 (mp) cc_final: 0.6030 (tp) REVERT: C 407 GLN cc_start: 0.6984 (mt0) cc_final: 0.6698 (mt0) REVERT: C 415 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: C 452 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (t70) REVERT: C 462 LEU cc_start: 0.7858 (mm) cc_final: 0.7637 (mp) REVERT: A 165 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: A 250 MET cc_start: 0.8974 (ttt) cc_final: 0.8769 (ttt) REVERT: A 326 ILE cc_start: 0.9110 (tt) cc_final: 0.8826 (tt) REVERT: B 393 GLU cc_start: 0.7946 (tp30) cc_final: 0.7495 (tp30) REVERT: B 397 GLN cc_start: 0.8752 (mp-120) cc_final: 0.8458 (mm110) REVERT: B 489 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8209 (ttmm) REVERT: F 17 LYS cc_start: 0.8516 (tttt) cc_final: 0.8062 (ttmt) REVERT: F 381 GLN cc_start: 0.7964 (tt0) cc_final: 0.7715 (tp40) REVERT: D 10 MET cc_start: 0.7930 (mtp) cc_final: 0.7584 (mtm) REVERT: D 144 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8167 (tm) REVERT: D 364 TYR cc_start: 0.8690 (t80) cc_final: 0.8468 (t80) REVERT: D 378 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8318 (tppt) REVERT: D 408 PHE cc_start: 0.8153 (m-80) cc_final: 0.7732 (m-80) REVERT: E 39 GLU cc_start: 0.7633 (pm20) cc_final: 0.7409 (pm20) REVERT: E 170 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6100 (tt0) REVERT: E 177 GLN cc_start: 0.8049 (mt0) cc_final: 0.7550 (mp10) REVERT: E 334 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7882 (ptmm) REVERT: G 22 LYS cc_start: 0.8045 (tttp) cc_final: 0.7767 (tppt) REVERT: G 120 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7296 (mtm110) REVERT: G 127 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7298 (ttm-80) REVERT: G 204 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6779 (tm-30) REVERT: H 4 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6303 (pp) REVERT: H 32 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7589 (tt) REVERT: I 88 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7244 (mm) outliers start: 97 outliers final: 80 residues processed: 526 average time/residue: 0.4525 time to fit residues: 392.9057 Evaluate side-chains 541 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 452 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 11 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 11 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain c3 residue 70 LEU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain c4 residue 61 ILE Chi-restraints excluded: chain c5 residue 48 MET Chi-restraints excluded: chain c6 residue 64 VAL Chi-restraints excluded: chain c7 residue 64 VAL Chi-restraints excluded: chain c8 residue 3 LEU Chi-restraints excluded: chain c8 residue 17 LEU Chi-restraints excluded: chain c0 residue 10 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 0.8980 chunk 392 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 369 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b2 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN A 15 GLN A 163 GLN ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126343 restraints weight = 39875.895| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.92 r_work: 0.3103 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35388 Z= 0.263 Angle : 0.683 22.772 48101 Z= 0.324 Chirality : 0.046 0.386 5774 Planarity : 0.004 0.074 6223 Dihedral : 5.982 80.371 5167 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.78 % Allowed : 17.69 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.44 (0.12), residues: 4646 helix: 1.20 (0.10), residues: 2504 sheet: -0.76 (0.22), residues: 528 loop : -0.67 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 206 HIS 0.007 0.001 HIS E 363 PHE 0.021 0.001 PHE D 408 TYR 0.016 0.001 TYR C 292 ARG 0.012 0.000 ARGb1 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9029.35 seconds wall clock time: 161 minutes 45.10 seconds (9705.10 seconds total)