Starting phenix.real_space_refine on Wed Feb 14 20:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emf_31191/02_2024/7emf_31191.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 396 5.16 5 C 39692 2.51 5 N 10786 2.21 5 O 11458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "N ARG 225": "NH1" <-> "NH2" Residue "N GLU 227": "OE1" <-> "OE2" Residue "N GLU 363": "OE1" <-> "OE2" Residue "N GLU 427": "OE1" <-> "OE2" Residue "N GLU 696": "OE1" <-> "OE2" Residue "N ARG 1209": "NH1" <-> "NH2" Residue "N ARG 1218": "NH1" <-> "NH2" Residue "N ARG 1222": "NH1" <-> "NH2" Residue "N ARG 1288": "NH1" <-> "NH2" Residue "O ARG 684": "NH1" <-> "NH2" Residue "O GLU 722": "OE1" <-> "OE2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 510": "OE1" <-> "OE2" Residue "P ARG 701": "NH1" <-> "NH2" Residue "P GLU 703": "OE1" <-> "OE2" Residue "P ARG 741": "NH1" <-> "NH2" Residue "P ARG 754": "NH1" <-> "NH2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q ARG 99": "NH1" <-> "NH2" Residue "Q GLU 186": "OE1" <-> "OE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "Q ARG 507": "NH1" <-> "NH2" Residue "Q GLU 631": "OE1" <-> "OE2" Residue "Q ARG 633": "NH1" <-> "NH2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R GLU 55": "OE1" <-> "OE2" Residue "R PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "T GLU 34": "OE1" <-> "OE2" Residue "T GLU 80": "OE1" <-> "OE2" Residue "T GLU 141": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 105": "OE1" <-> "OE2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 31": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 313": "OE1" <-> "OE2" Residue "W PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 813": "NH1" <-> "NH2" Residue "W GLU 906": "OE1" <-> "OE2" Residue "W GLU 930": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X GLU 166": "OE1" <-> "OE2" Residue "X GLU 216": "OE1" <-> "OE2" Residue "X GLU 251": "OE1" <-> "OE2" Residue "X GLU 259": "OE1" <-> "OE2" Residue "X GLU 301": "OE1" <-> "OE2" Residue "X GLU 433": "OE1" <-> "OE2" Residue "X ARG 489": "NH1" <-> "NH2" Residue "X GLU 515": "OE1" <-> "OE2" Residue "X GLU 593": "OE1" <-> "OE2" Residue "X ARG 979": "NH1" <-> "NH2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 79": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Z ARG 545": "NH1" <-> "NH2" Residue "Z GLU 546": "OE1" <-> "OE2" Residue "0 GLU 12": "OE1" <-> "OE2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "0 GLU 69": "OE1" <-> "OE2" Residue "0 GLU 224": "OE1" <-> "OE2" Residue "0 ARG 271": "NH1" <-> "NH2" Residue "1 GLU 108": "OE1" <-> "OE2" Residue "1 GLU 117": "OE1" <-> "OE2" Residue "3 ARG 56": "NH1" <-> "NH2" Residue "3 GLU 141": "OE1" <-> "OE2" Residue "3 GLU 144": "OE1" <-> "OE2" Residue "4 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62334 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3578 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 30, 'TRANS': 436} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1268 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1374 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain breaks: 1 Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1348 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 10, 'TRANS': 150} Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Chain: "I" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 605 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "J" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 840 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "N" Number of atoms: 7772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7772 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 61, 'TRANS': 955} Chain breaks: 10 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "O" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1226 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 16, 'TRANS': 140} Chain breaks: 1 Chain: "P" Number of atoms: 5983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5983 Classifications: {'peptide': 766} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 4 Chain: "Q" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4361 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain breaks: 5 Chain: "R" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1532 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "S" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 476 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "T" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1499 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "U" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "V" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1063 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain: "W" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10774 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 70, 'TRANS': 1263} Chain: "X" Number of atoms: 7061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7061 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 35, 'TRANS': 861} Chain breaks: 9 Chain: "Y" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1605 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 15, 'TRANS': 194} Chain breaks: 1 Chain: "Z" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain breaks: 1 Chain: "0" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2159 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 2 Chain: "1" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "2" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain breaks: 1 Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1022 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 3 Chain: "4" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 986 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26042 SG CYS P 798 138.828 251.501 60.753 1.00 61.26 S ATOM 26066 SG CYS P 801 141.463 249.004 61.101 1.00 68.86 S ATOM 26279 SG CYS P 827 142.780 252.646 61.643 1.00 67.73 S ATOM 26293 SG CYS P 829 141.139 251.768 58.034 1.00 67.16 S ATOM 58363 SG CYS 0 281 116.315 210.661 125.061 1.00 78.68 S ATOM 58389 SG CYS 0 284 115.359 213.470 127.432 1.00 81.40 S ATOM 58597 SG CYS 0 309 112.171 211.559 125.450 1.00 79.33 S Time building chain proxies: 25.16, per 1000 atoms: 0.40 Number of scatterers: 62334 At special positions: 0 Unit cell: (199.206, 381.548, 236.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 396 16.00 O 11458 8.00 N 10786 7.00 C 39692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.71 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 401 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 281 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 284 " pdb="ZN ZN 0 401 " - pdb=" SG CYS 0 309 " pdb=" ZN P 901 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 829 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 827 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 798 " pdb="ZN ZN P 901 " - pdb=" SG CYS P 801 " Number of angles added : 6 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15156 Finding SS restraints... Secondary structure from input PDB file: 302 helices and 40 sheets defined 58.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 removed outlier: 3.824A pdb=" N SER A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.680A pdb=" N GLU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.612A pdb=" N PHE A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.940A pdb=" N LEU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.650A pdb=" N THR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'D' and resid 27 through 52 Processing helix chain 'D' and resid 63 through 141 removed outlier: 4.019A pdb=" N GLN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'F' and resid 9 through 13 removed outlier: 3.652A pdb=" N ILE F 13 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 25 through 33 removed outlier: 4.097A pdb=" N LEU F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 4.005A pdb=" N VAL F 49 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.826A pdb=" N VAL F 114 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 135 " --> pdb=" O ASP F 131 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.958A pdb=" N THR G 22 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 99 Processing helix chain 'G' and resid 103 through 125 removed outlier: 3.645A pdb=" N GLU G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 175 removed outlier: 4.557A pdb=" N HIS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Proline residue: G 172 - end of helix Processing helix chain 'H' and resid 4 through 36 Processing helix chain 'H' and resid 41 through 66 removed outlier: 3.578A pdb=" N GLU H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.634A pdb=" N GLU H 94 " --> pdb=" O MET H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 114 through 129 Processing helix chain 'H' and resid 134 through 158 Processing helix chain 'H' and resid 174 through 187 removed outlier: 3.559A pdb=" N PHE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 86 through 102 Processing helix chain 'I' and resid 110 through 138 Processing helix chain 'J' and resid 8 through 29 Processing helix chain 'J' and resid 35 through 60 removed outlier: 3.990A pdb=" N GLN J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 removed outlier: 4.042A pdb=" N PHE J 68 " --> pdb=" O PRO J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 117 Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.553A pdb=" N MET J 121 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 35 Processing helix chain 'K' and resid 41 through 73 Processing helix chain 'K' and resid 83 through 116 removed outlier: 3.768A pdb=" N ARG K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 73 Processing helix chain 'N' and resid 77 through 106 removed outlier: 3.897A pdb=" N ILE N 83 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 142 removed outlier: 3.600A pdb=" N VAL N 112 " --> pdb=" O ASN N 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP N 142 " --> pdb=" O SER N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 162 removed outlier: 3.789A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 178 Processing helix chain 'N' and resid 186 through 204 Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 267 through 284 Processing helix chain 'N' and resid 287 through 318 removed outlier: 3.860A pdb=" N ASP N 291 " --> pdb=" O LYS N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 389 removed outlier: 3.708A pdb=" N GLU N 387 " --> pdb=" O SER N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 424 removed outlier: 3.529A pdb=" N LEU N 400 " --> pdb=" O SER N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 485 Processing helix chain 'N' and resid 488 through 507 removed outlier: 3.899A pdb=" N TRP N 492 " --> pdb=" O ARG N 488 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN N 494 " --> pdb=" O ILE N 490 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE N 498 " --> pdb=" O GLN N 494 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP N 499 " --> pdb=" O GLN N 495 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.595A pdb=" N ALA N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 664 removed outlier: 4.038A pdb=" N GLY N 656 " --> pdb=" O MET N 652 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU N 657 " --> pdb=" O PRO N 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU N 664 " --> pdb=" O GLU N 660 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 702 Processing helix chain 'N' and resid 714 through 718 removed outlier: 4.184A pdb=" N ARG N 718 " --> pdb=" O ARG N 715 " (cutoff:3.500A) Processing helix chain 'N' and resid 759 through 787 removed outlier: 3.841A pdb=" N VAL N 763 " --> pdb=" O GLY N 759 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS N 779 " --> pdb=" O ARG N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 797 Processing helix chain 'N' and resid 851 through 862 Processing helix chain 'N' and resid 864 through 883 removed outlier: 5.043A pdb=" N ALA N 877 " --> pdb=" O PHE N 873 " (cutoff:3.500A) Proline residue: N 878 - end of helix removed outlier: 3.647A pdb=" N ALA N 881 " --> pdb=" O ALA N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 958 through 967 removed outlier: 3.541A pdb=" N PHE N 962 " --> pdb=" O GLY N 958 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE N 966 " --> pdb=" O PHE N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 1179 through 1187 Processing helix chain 'N' and resid 1205 through 1226 Processing helix chain 'N' and resid 1276 through 1289 Processing helix chain 'N' and resid 1295 through 1306 removed outlier: 4.023A pdb=" N LEU N1299 " --> pdb=" O LYS N1295 " (cutoff:3.500A) Processing helix chain 'N' and resid 1311 through 1325 Processing helix chain 'O' and resid 618 through 628 removed outlier: 3.612A pdb=" N LEU O 622 " --> pdb=" O CYS O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 633 through 650 Proline residue: O 644 - end of helix Processing helix chain 'O' and resid 675 through 684 removed outlier: 3.535A pdb=" N GLN O 679 " --> pdb=" O PRO O 675 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG O 684 " --> pdb=" O GLY O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 746 through 762 Processing helix chain 'O' and resid 768 through 788 removed outlier: 4.020A pdb=" N LEU O 772 " --> pdb=" O SER O 768 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA O 787 " --> pdb=" O ALA O 783 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 59 Processing helix chain 'P' and resid 147 through 150 Processing helix chain 'P' and resid 154 through 158 Processing helix chain 'P' and resid 364 through 374 Processing helix chain 'P' and resid 466 through 484 Processing helix chain 'P' and resid 488 through 493 Processing helix chain 'P' and resid 496 through 498 No H-bonds generated for 'chain 'P' and resid 496 through 498' Processing helix chain 'P' and resid 499 through 512 Processing helix chain 'P' and resid 517 through 522 Processing helix chain 'P' and resid 522 through 535 Processing helix chain 'P' and resid 540 through 542 No H-bonds generated for 'chain 'P' and resid 540 through 542' Processing helix chain 'P' and resid 543 through 564 removed outlier: 3.997A pdb=" N THR P 559 " --> pdb=" O ALA P 555 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU P 564 " --> pdb=" O LEU P 560 " (cutoff:3.500A) Processing helix chain 'P' and resid 575 through 587 Processing helix chain 'P' and resid 591 through 598 removed outlier: 3.821A pdb=" N VAL P 595 " --> pdb=" O ASP P 591 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN P 598 " --> pdb=" O LYS P 594 " (cutoff:3.500A) Processing helix chain 'P' and resid 609 through 614 Processing helix chain 'P' and resid 614 through 632 Processing helix chain 'P' and resid 648 through 669 Processing helix chain 'P' and resid 670 through 673 removed outlier: 3.726A pdb=" N LEU P 673 " --> pdb=" O PRO P 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 670 through 673' Processing helix chain 'P' and resid 684 through 701 removed outlier: 4.136A pdb=" N CYS P 699 " --> pdb=" O LYS P 695 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS P 700 " --> pdb=" O LEU P 696 " (cutoff:3.500A) Processing helix chain 'P' and resid 710 through 719 Processing helix chain 'P' and resid 719 through 724 Processing helix chain 'P' and resid 737 through 742 removed outlier: 3.936A pdb=" N ARG P 741 " --> pdb=" O GLY P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 821 Processing helix chain 'Q' and resid 36 through 47 removed outlier: 3.644A pdb=" N LEU Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 121 Processing helix chain 'Q' and resid 139 through 172 removed outlier: 3.591A pdb=" N THR Q 143 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 194 Processing helix chain 'Q' and resid 290 through 318 removed outlier: 3.779A pdb=" N LYS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 387 removed outlier: 3.941A pdb=" N GLU Q 372 " --> pdb=" O LEU Q 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR Q 386 " --> pdb=" O PHE Q 382 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 387 " --> pdb=" O HIS Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 392 removed outlier: 3.710A pdb=" N MET Q 391 " --> pdb=" O SER Q 388 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 414 through 422 removed outlier: 3.541A pdb=" N ILE Q 418 " --> pdb=" O ASP Q 414 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 455 removed outlier: 3.575A pdb=" N LYS Q 430 " --> pdb=" O GLY Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 544 removed outlier: 3.923A pdb=" N VAL Q 534 " --> pdb=" O SER Q 530 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL Q 537 " --> pdb=" O GLN Q 533 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL Q 543 " --> pdb=" O GLN Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 617 Processing helix chain 'Q' and resid 635 through 646 Processing helix chain 'R' and resid 28 through 43 removed outlier: 4.485A pdb=" N GLU R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER R 34 " --> pdb=" O HIS R 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU R 35 " --> pdb=" O SER R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 122 removed outlier: 3.539A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 192 Processing helix chain 'S' and resid 82 through 87 Processing helix chain 'S' and resid 89 through 97 Processing helix chain 'S' and resid 112 through 117 Processing helix chain 'S' and resid 128 through 139 Proline residue: S 134 - end of helix Processing helix chain 'S' and resid 147 through 153 Processing helix chain 'T' and resid 16 through 32 Processing helix chain 'T' and resid 90 through 99 Processing helix chain 'T' and resid 153 through 165 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.654A pdb=" N ASN T 178 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 204 removed outlier: 4.107A pdb=" N THR T 189 " --> pdb=" O GLY T 185 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET T 190 " --> pdb=" O PRO T 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 82 through 133 Processing helix chain 'V' and resid 11 through 40 Processing helix chain 'V' and resid 49 through 90 Processing helix chain 'V' and resid 90 through 136 removed outlier: 3.689A pdb=" N VAL V 94 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 removed outlier: 3.635A pdb=" N VAL W 13 " --> pdb=" O PHE W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 51 Processing helix chain 'W' and resid 57 through 69 Processing helix chain 'W' and resid 72 through 89 Processing helix chain 'W' and resid 95 through 103 Processing helix chain 'W' and resid 111 through 126 Processing helix chain 'W' and resid 127 through 129 No H-bonds generated for 'chain 'W' and resid 127 through 129' Processing helix chain 'W' and resid 130 through 146 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.709A pdb=" N GLU W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.587A pdb=" N ALA W 183 " --> pdb=" O PRO W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 removed outlier: 4.202A pdb=" N PHE W 208 " --> pdb=" O LEU W 204 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 219 removed outlier: 3.565A pdb=" N ALA W 216 " --> pdb=" O PHE W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 227 removed outlier: 3.715A pdb=" N LEU W 227 " --> pdb=" O ARG W 224 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 264 Processing helix chain 'W' and resid 266 through 275 removed outlier: 3.841A pdb=" N LEU W 270 " --> pdb=" O GLN W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 288 Processing helix chain 'W' and resid 297 through 318 removed outlier: 4.518A pdb=" N GLU W 318 " --> pdb=" O ARG W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 344 Processing helix chain 'W' and resid 348 through 361 removed outlier: 3.669A pdb=" N MET W 352 " --> pdb=" O SER W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 368 through 384 removed outlier: 3.570A pdb=" N LEU W 372 " --> pdb=" O GLY W 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 393 removed outlier: 4.134A pdb=" N PHE W 392 " --> pdb=" O ALA W 388 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 403 removed outlier: 3.844A pdb=" N LEU W 398 " --> pdb=" O PRO W 394 " (cutoff:3.500A) Processing helix chain 'W' and resid 418 through 423 Processing helix chain 'W' and resid 423 through 437 Processing helix chain 'W' and resid 451 through 464 Processing helix chain 'W' and resid 472 through 481 Processing helix chain 'W' and resid 488 through 501 removed outlier: 3.901A pdb=" N ALA W 494 " --> pdb=" O LEU W 490 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR W 498 " --> pdb=" O ALA W 494 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE W 499 " --> pdb=" O LEU W 495 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 530 Processing helix chain 'W' and resid 532 through 553 Processing helix chain 'W' and resid 560 through 571 Processing helix chain 'W' and resid 573 through 579 removed outlier: 3.640A pdb=" N ILE W 576 " --> pdb=" O TYR W 573 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU W 577 " --> pdb=" O MET W 574 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER W 578 " --> pdb=" O GLU W 575 " (cutoff:3.500A) Processing helix chain 'W' and resid 580 through 587 Processing helix chain 'W' and resid 587 through 595 Processing helix chain 'W' and resid 599 through 611 Processing helix chain 'W' and resid 616 through 633 Processing helix chain 'W' and resid 638 through 654 Processing helix chain 'W' and resid 660 through 666 Processing helix chain 'W' and resid 671 through 676 removed outlier: 3.574A pdb=" N THR W 674 " --> pdb=" O ASP W 671 " (cutoff:3.500A) Processing helix chain 'W' and resid 680 through 698 removed outlier: 4.151A pdb=" N ASN W 684 " --> pdb=" O SER W 680 " (cutoff:3.500A) Processing helix chain 'W' and resid 710 through 721 removed outlier: 4.375A pdb=" N ASP W 714 " --> pdb=" O THR W 710 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE W 715 " --> pdb=" O TRP W 711 " (cutoff:3.500A) Processing helix chain 'W' and resid 728 through 733 Processing helix chain 'W' and resid 736 through 745 removed outlier: 3.945A pdb=" N GLN W 745 " --> pdb=" O ALA W 741 " (cutoff:3.500A) Processing helix chain 'W' and resid 752 through 770 Processing helix chain 'W' and resid 772 through 781 removed outlier: 3.623A pdb=" N SER W 781 " --> pdb=" O ILE W 777 " (cutoff:3.500A) Processing helix chain 'W' and resid 788 through 800 removed outlier: 3.755A pdb=" N GLU W 799 " --> pdb=" O LYS W 795 " (cutoff:3.500A) Processing helix chain 'W' and resid 805 through 815 removed outlier: 3.861A pdb=" N ARG W 809 " --> pdb=" O GLN W 805 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY W 815 " --> pdb=" O LEU W 811 " (cutoff:3.500A) Processing helix chain 'W' and resid 815 through 837 removed outlier: 3.605A pdb=" N LEU W 819 " --> pdb=" O GLY W 815 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL W 820 " --> pdb=" O ALA W 816 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA W 821 " --> pdb=" O ARG W 817 " (cutoff:3.500A) Processing helix chain 'W' and resid 840 through 855 Processing helix chain 'W' and resid 861 through 871 Processing helix chain 'W' and resid 876 through 892 Processing helix chain 'W' and resid 896 through 906 removed outlier: 3.652A pdb=" N GLU W 906 " --> pdb=" O ASP W 902 " (cutoff:3.500A) Processing helix chain 'W' and resid 916 through 928 removed outlier: 3.752A pdb=" N LYS W 920 " --> pdb=" O ASP W 916 " (cutoff:3.500A) Processing helix chain 'W' and resid 934 through 941 Processing helix chain 'W' and resid 959 through 977 removed outlier: 3.872A pdb=" N LEU W 964 " --> pdb=" O CYS W 960 " (cutoff:3.500A) Proline residue: W 965 - end of helix Processing helix chain 'W' and resid 980 through 991 removed outlier: 3.671A pdb=" N LEU W 984 " --> pdb=" O VAL W 980 " (cutoff:3.500A) Processing helix chain 'W' and resid 992 through 998 Processing helix chain 'W' and resid 1000 through 1012 Processing helix chain 'W' and resid 1019 through 1033 removed outlier: 3.557A pdb=" N LYS W1023 " --> pdb=" O ARG W1019 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1052 removed outlier: 3.543A pdb=" N CYS W1051 " --> pdb=" O THR W1047 " (cutoff:3.500A) Processing helix chain 'W' and resid 1064 through 1081 removed outlier: 3.698A pdb=" N TYR W1068 " --> pdb=" O ASP W1064 " (cutoff:3.500A) Processing helix chain 'W' and resid 1091 through 1095 removed outlier: 3.818A pdb=" N ASN W1095 " --> pdb=" O TRP W1092 " (cutoff:3.500A) Processing helix chain 'W' and resid 1099 through 1114 removed outlier: 3.631A pdb=" N HIS W1103 " --> pdb=" O ASN W1099 " (cutoff:3.500A) Processing helix chain 'W' and resid 1118 through 1131 removed outlier: 4.220A pdb=" N VAL W1130 " --> pdb=" O LEU W1126 " (cutoff:3.500A) Processing helix chain 'W' and resid 1141 through 1155 removed outlier: 3.750A pdb=" N TRP W1145 " --> pdb=" O ASN W1141 " (cutoff:3.500A) Processing helix chain 'W' and resid 1157 through 1162 removed outlier: 3.573A pdb=" N TRP W1161 " --> pdb=" O PRO W1157 " (cutoff:3.500A) Processing helix chain 'W' and resid 1162 through 1173 removed outlier: 4.052A pdb=" N ASP W1166 " --> pdb=" O ILE W1162 " (cutoff:3.500A) Processing helix chain 'W' and resid 1186 through 1191 Processing helix chain 'W' and resid 1192 through 1198 Processing helix chain 'W' and resid 1203 through 1218 removed outlier: 3.707A pdb=" N HIS W1218 " --> pdb=" O ALA W1214 " (cutoff:3.500A) Processing helix chain 'W' and resid 1220 through 1225 Processing helix chain 'W' and resid 1226 through 1234 Processing helix chain 'W' and resid 1241 through 1253 Processing helix chain 'W' and resid 1255 through 1263 Processing helix chain 'W' and resid 1263 through 1284 removed outlier: 4.114A pdb=" N MET W1267 " --> pdb=" O ARG W1263 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE W1268 " --> pdb=" O THR W1264 " (cutoff:3.500A) Processing helix chain 'W' and resid 1290 through 1305 removed outlier: 3.556A pdb=" N ILE W1294 " --> pdb=" O TYR W1290 " (cutoff:3.500A) Processing helix chain 'W' and resid 1311 through 1320 removed outlier: 3.645A pdb=" N GLU W1315 " --> pdb=" O LYS W1311 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS W1316 " --> pdb=" O GLU W1312 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE W1317 " --> pdb=" O GLN W1313 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN W1320 " --> pdb=" O LYS W1316 " (cutoff:3.500A) Processing helix chain 'W' and resid 1322 through 1330 Processing helix chain 'W' and resid 1331 through 1334 removed outlier: 3.624A pdb=" N HIS W1334 " --> pdb=" O PHE W1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1331 through 1334' Processing helix chain 'X' and resid 5 through 16 Processing helix chain 'X' and resid 19 through 31 Processing helix chain 'X' and resid 34 through 38 removed outlier: 3.580A pdb=" N ASP X 38 " --> pdb=" O ALA X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 49 Processing helix chain 'X' and resid 57 through 70 Processing helix chain 'X' and resid 74 through 84 removed outlier: 3.547A pdb=" N VAL X 78 " --> pdb=" O SER X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 105 removed outlier: 3.635A pdb=" N VAL X 94 " --> pdb=" O ARG X 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE X 104 " --> pdb=" O ILE X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 146 Processing helix chain 'X' and resid 156 through 171 removed outlier: 4.112A pdb=" N SER X 171 " --> pdb=" O LYS X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 185 removed outlier: 4.247A pdb=" N LEU X 183 " --> pdb=" O HIS X 179 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU X 184 " --> pdb=" O ILE X 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU X 185 " --> pdb=" O ALA X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 206 removed outlier: 3.743A pdb=" N ALA X 191 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU X 206 " --> pdb=" O ILE X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 225 Processing helix chain 'X' and resid 241 through 254 removed outlier: 3.736A pdb=" N HIS X 245 " --> pdb=" O PHE X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 259 through 274 removed outlier: 3.736A pdb=" N LEU X 263 " --> pdb=" O GLU X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 277 through 295 Processing helix chain 'X' and resid 299 through 311 removed outlier: 3.561A pdb=" N LEU X 303 " --> pdb=" O GLY X 299 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 324 Processing helix chain 'X' and resid 330 through 343 Processing helix chain 'X' and resid 344 through 356 Processing helix chain 'X' and resid 358 through 370 removed outlier: 3.990A pdb=" N PHE X 362 " --> pdb=" O ASP X 358 " (cutoff:3.500A) Processing helix chain 'X' and resid 374 through 391 removed outlier: 4.085A pdb=" N HIS X 391 " --> pdb=" O ALA X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 424 Proline residue: X 415 - end of helix Processing helix chain 'X' and resid 426 through 431 Processing helix chain 'X' and resid 431 through 444 Processing helix chain 'X' and resid 446 through 458 Processing helix chain 'X' and resid 460 through 478 removed outlier: 4.614A pdb=" N TYR X 477 " --> pdb=" O GLU X 473 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY X 478 " --> pdb=" O PHE X 474 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 507 removed outlier: 3.974A pdb=" N LEU X 491 " --> pdb=" O SER X 487 " (cutoff:3.500A) Processing helix chain 'X' and resid 523 through 533 removed outlier: 3.516A pdb=" N THR X 527 " --> pdb=" O PRO X 523 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET X 533 " --> pdb=" O MET X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 548 Processing helix chain 'X' and resid 551 through 562 removed outlier: 3.731A pdb=" N GLU X 555 " --> pdb=" O SER X 551 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER X 556 " --> pdb=" O THR X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 573 through 595 removed outlier: 4.880A pdb=" N SER X 582 " --> pdb=" O CYS X 578 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA X 583 " --> pdb=" O LEU X 579 " (cutoff:3.500A) Processing helix chain 'X' and resid 598 through 611 Processing helix chain 'X' and resid 614 through 631 Processing helix chain 'X' and resid 636 through 647 removed outlier: 3.902A pdb=" N GLN X 641 " --> pdb=" O GLU X 637 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET X 642 " --> pdb=" O LYS X 638 " (cutoff:3.500A) Processing helix chain 'X' and resid 658 through 675 Processing helix chain 'X' and resid 676 through 681 removed outlier: 3.516A pdb=" N THR X 681 " --> pdb=" O VAL X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 706 through 722 removed outlier: 3.835A pdb=" N VAL X 710 " --> pdb=" O PRO X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 754 removed outlier: 3.527A pdb=" N ILE X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL X 741 " --> pdb=" O HIS X 737 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N TYR X 742 " --> pdb=" O MET X 738 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP X 743 " --> pdb=" O GLY X 739 " (cutoff:3.500A) Processing helix chain 'X' and resid 757 through 773 removed outlier: 4.223A pdb=" N SER X 770 " --> pdb=" O GLU X 766 " (cutoff:3.500A) Processing helix chain 'X' and resid 775 through 786 Processing helix chain 'X' and resid 786 through 794 Processing helix chain 'X' and resid 796 through 801 removed outlier: 4.115A pdb=" N HIS X 799 " --> pdb=" O SER X 796 " (cutoff:3.500A) Processing helix chain 'X' and resid 802 through 823 removed outlier: 4.030A pdb=" N ALA X 808 " --> pdb=" O PRO X 804 " (cutoff:3.500A) Processing helix chain 'X' and resid 829 through 839 Processing helix chain 'X' and resid 842 through 847 Processing helix chain 'X' and resid 895 through 914 removed outlier: 3.538A pdb=" N ARG X 899 " --> pdb=" O ASP X 895 " (cutoff:3.500A) Processing helix chain 'X' and resid 918 through 935 removed outlier: 3.532A pdb=" N GLN X 922 " --> pdb=" O GLY X 918 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU X 935 " --> pdb=" O CYS X 931 " (cutoff:3.500A) Processing helix chain 'X' and resid 942 through 947 Processing helix chain 'X' and resid 949 through 958 removed outlier: 4.020A pdb=" N SER X 953 " --> pdb=" O PHE X 949 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL X 956 " --> pdb=" O VAL X 952 " (cutoff:3.500A) Processing helix chain 'X' and resid 966 through 970 Processing helix chain 'X' and resid 975 through 988 removed outlier: 4.075A pdb=" N GLN X 980 " --> pdb=" O PRO X 976 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 39 Processing helix chain 'Y' and resid 39 through 48 Processing helix chain 'Y' and resid 90 through 101 removed outlier: 3.509A pdb=" N PHE Y 94 " --> pdb=" O SER Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 132 removed outlier: 3.561A pdb=" N GLY Y 117 " --> pdb=" O LEU Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 176 through 178 No H-bonds generated for 'chain 'Y' and resid 176 through 178' Processing helix chain 'Y' and resid 188 through 198 removed outlier: 3.695A pdb=" N ARG Y 192 " --> pdb=" O LEU Y 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 484 through 500 Processing helix chain 'Z' and resid 549 through 557 Processing helix chain '0' and resid 8 through 38 removed outlier: 3.613A pdb=" N GLY 0 38 " --> pdb=" O CYS 0 34 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 77 Processing helix chain '0' and resid 104 through 131 removed outlier: 3.696A pdb=" N GLN 0 131 " --> pdb=" O LEU 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 172 removed outlier: 3.569A pdb=" N VAL 0 162 " --> pdb=" O PRO 0 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET 0 172 " --> pdb=" O ARG 0 168 " (cutoff:3.500A) Processing helix chain '0' and resid 236 through 253 removed outlier: 3.645A pdb=" N GLN 0 240 " --> pdb=" O TYR 0 236 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 272 removed outlier: 3.740A pdb=" N SER 0 272 " --> pdb=" O THR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 276 Processing helix chain '0' and resid 306 through 310 Processing helix chain '1' and resid 43 through 56 removed outlier: 3.709A pdb=" N GLU 1 47 " --> pdb=" O THR 1 43 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE 1 56 " --> pdb=" O PHE 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 106 Processing helix chain '1' and resid 107 through 144 Processing helix chain '2' and resid 56 through 90 Proline residue: 2 65 - end of helix Processing helix chain '2' and resid 101 through 136 removed outlier: 4.238A pdb=" N CYS 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 186 removed outlier: 4.328A pdb=" N THR 2 186 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 58 removed outlier: 4.529A pdb=" N ARG 3 35 " --> pdb=" O ALA 3 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR 3 46 " --> pdb=" O GLN 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 102 Processing helix chain '3' and resid 137 through 176 Processing helix chain '4' and resid 11 through 29 Processing helix chain '4' and resid 30 through 40 Processing helix chain '4' and resid 45 through 55 removed outlier: 3.674A pdb=" N VAL 4 49 " --> pdb=" O ASP 4 45 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 59 Processing helix chain '4' and resid 60 through 65 Processing helix chain '4' and resid 71 through 80 Processing helix chain '4' and resid 82 through 87 removed outlier: 3.600A pdb=" N LYS 4 86 " --> pdb=" O GLU 4 82 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 106 removed outlier: 3.619A pdb=" N ALA 4 94 " --> pdb=" O ASN 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 106 through 122 removed outlier: 3.820A pdb=" N GLN 4 122 " --> pdb=" O ALA 4 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.665A pdb=" N TYR A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN A 221 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 257 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS A 223 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 255 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 225 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ASN A 254 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 394 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLN A 309 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LEU A 392 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ILE A 311 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N GLY A 390 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.503A pdb=" N VAL A 297 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.176A pdb=" N GLN A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE A 440 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS A 373 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 442 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 375 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN A 439 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN A 455 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 445 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'F' and resid 66 through 73 removed outlier: 6.326A pdb=" N ILE F 80 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE F 79 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN F 85 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN F 87 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL F 92 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'N' and resid 224 through 226 removed outlier: 3.625A pdb=" N PHE N 230 " --> pdb=" O VAL N 226 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS N 249 " --> pdb=" O THR N 233 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR N 235 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU N 247 " --> pdb=" O THR N 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 324 through 330 removed outlier: 6.645A pdb=" N SER N 336 " --> pdb=" O GLU N 327 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR N 329 " --> pdb=" O CYS N 334 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS N 334 " --> pdb=" O TYR N 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 430 through 432 Processing sheet with id=AB3, first strand: chain 'N' and resid 514 through 517 removed outlier: 5.269A pdb=" N TYR N 548 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER N 572 " --> pdb=" O LEU N 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 682 through 683 removed outlier: 5.296A pdb=" N LEU N 705 " --> pdb=" O ALA N 727 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA N 727 " --> pdb=" O LEU N 705 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP N 707 " --> pdb=" O VAL N 725 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR N 709 " --> pdb=" O GLU N 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 798 through 803 removed outlier: 5.327A pdb=" N VAL N 800 " --> pdb=" O CYS N 811 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS N 811 " --> pdb=" O VAL N 800 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 904 through 908 removed outlier: 4.241A pdb=" N VAL N 933 " --> pdb=" O ARG N 929 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 1240 through 1242 Processing sheet with id=AB8, first strand: chain 'N' and resid 1338 through 1339 Processing sheet with id=AB9, first strand: chain 'O' and resid 692 through 693 removed outlier: 4.441A pdb=" N GLU O 722 " --> pdb=" O ILE O 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 431 through 436 removed outlier: 6.489A pdb=" N ILE P 446 " --> pdb=" O LYS P 432 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET P 434 " --> pdb=" O VAL P 444 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL P 444 " --> pdb=" O MET P 434 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU P 436 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA P 442 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR P 17 " --> pdb=" O VAL P 454 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG P 456 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU P 15 " --> pdb=" O ARG P 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'P' and resid 84 through 89 removed outlier: 6.443A pdb=" N ILE P 105 " --> pdb=" O GLY P 123 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY P 123 " --> pdb=" O ILE P 105 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYS P 107 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER P 121 " --> pdb=" O CYS P 107 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER P 117 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 131 through 136 removed outlier: 6.454A pdb=" N VAL P 182 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU P 134 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE P 180 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP P 136 " --> pdb=" O GLY P 178 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY P 178 " --> pdb=" O TRP P 136 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU P 177 " --> pdb=" O LEU P 193 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 143 through 145 Processing sheet with id=AC6, first strand: chain 'P' and resid 215 through 220 Processing sheet with id=AC7, first strand: chain 'P' and resid 279 through 287 removed outlier: 5.182A pdb=" N ILE P 280 " --> pdb=" O SER P 299 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER P 299 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS P 282 " --> pdb=" O CYS P 297 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN P 293 " --> pdb=" O LEU P 286 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL P 306 " --> pdb=" O ALA P 344 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA P 344 " --> pdb=" O VAL P 306 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS P 308 " --> pdb=" O LEU P 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 351 through 355 removed outlier: 4.111A pdb=" N ALA P 353 " --> pdb=" O ALA P 385 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 391 " --> pdb=" O VAL P 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL P 404 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE P 393 " --> pdb=" O MET P 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 804 through 806 removed outlier: 4.549A pdb=" N CYS P 795 " --> pdb=" O VAL P 836 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 195 through 199 removed outlier: 4.555A pdb=" N LYS Q 195 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE Q 203 " --> pdb=" O VAL Q 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 255 through 262 Processing sheet with id=AD3, first strand: chain 'Q' and resid 461 through 462 Processing sheet with id=AD4, first strand: chain 'Q' and resid 461 through 462 removed outlier: 3.767A pdb=" N ILE Q 502 " --> pdb=" O LEU Q 514 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 547 through 555 removed outlier: 6.824A pdb=" N LEU Q 549 " --> pdb=" O ALA Q 572 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA Q 572 " --> pdb=" O LEU Q 549 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE Q 551 " --> pdb=" O THR Q 570 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR Q 570 " --> pdb=" O PHE Q 551 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN Q 553 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA Q 568 " --> pdb=" O ASN Q 553 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA Q 566 " --> pdb=" O VAL Q 555 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR Q 578 " --> pdb=" O SER Q 573 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 160 through 162 removed outlier: 4.325A pdb=" N MET R 18 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU R 88 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL R 69 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS R 127 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU R 59 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET R 125 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU R 128 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE R 151 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 3 through 9 removed outlier: 3.897A pdb=" N ILE T 138 " --> pdb=" O MET T 9 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER T 134 " --> pdb=" O MET T 131 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL T 129 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE T 138 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY T 127 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL T 140 " --> pdb=" O LYS T 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS T 125 " --> pdb=" O VAL T 140 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 142 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU T 123 " --> pdb=" O VAL T 142 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL T 126 " --> pdb=" O THR T 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR T 115 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG T 113 " --> pdb=" O THR T 128 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU T 111 " --> pdb=" O THR T 130 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY T 37 " --> pdb=" O ARG T 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLN T 118 " --> pdb=" O LYS T 35 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS T 35 " --> pdb=" O GLN T 118 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 506 through 507 removed outlier: 7.013A pdb=" N MET W 515 " --> pdb=" O ALA W 558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 83 through 84 removed outlier: 6.038A pdb=" N ASP Y 17 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU Y 143 " --> pdb=" O ASP Y 17 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL Y 19 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE Y 145 " --> pdb=" O VAL Y 19 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL Y 21 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 565 through 566 Processing sheet with id=AE2, first strand: chain 'Z' and resid 580 through 582 Processing sheet with id=AE3, first strand: chain '0' and resid 176 through 181 Processing sheet with id=AE4, first strand: chain '0' and resid 296 through 297 3673 hydrogen bonds defined for protein. 10713 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: 23.48 Time building geometry restraints manager: 20.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10377 1.31 - 1.44: 16189 1.44 - 1.57: 36402 1.57 - 1.70: 0 1.70 - 1.83: 604 Bond restraints: 63572 Sorted by residual: bond pdb=" C VAL O 643 " pdb=" N PRO O 644 " ideal model delta sigma weight residual 1.336 1.394 -0.059 1.23e-02 6.61e+03 2.28e+01 bond pdb=" C PRO X 432 " pdb=" O PRO X 432 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" N VAL T 148 " pdb=" CA VAL T 148 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.67e+01 bond pdb=" N ILE A 270 " pdb=" CA ILE A 270 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.09e-02 8.42e+03 1.66e+01 bond pdb=" N LEU U 76 " pdb=" CA LEU U 76 " ideal model delta sigma weight residual 1.457 1.514 -0.057 1.41e-02 5.03e+03 1.63e+01 ... (remaining 63567 not shown) Histogram of bond angle deviations from ideal: 97.12 - 105.35: 1510 105.35 - 113.57: 36778 113.57 - 121.80: 35396 121.80 - 130.03: 11899 130.03 - 138.26: 523 Bond angle restraints: 86106 Sorted by residual: angle pdb=" N PRO N1351 " pdb=" CA PRO N1351 " pdb=" CB PRO N1351 " ideal model delta sigma weight residual 103.08 112.14 -9.06 9.70e-01 1.06e+00 8.72e+01 angle pdb=" N PRO N1343 " pdb=" CA PRO N1343 " pdb=" CB PRO N1343 " ideal model delta sigma weight residual 103.08 112.06 -8.98 9.70e-01 1.06e+00 8.56e+01 angle pdb=" N HIS 4 83 " pdb=" CA HIS 4 83 " pdb=" C HIS 4 83 " ideal model delta sigma weight residual 112.90 100.97 11.93 1.31e+00 5.83e-01 8.29e+01 angle pdb=" N GLN F 173 " pdb=" CA GLN F 173 " pdb=" C GLN F 173 " ideal model delta sigma weight residual 112.94 100.92 12.02 1.41e+00 5.03e-01 7.27e+01 angle pdb=" N PRO N1355 " pdb=" CA PRO N1355 " pdb=" CB PRO N1355 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 ... (remaining 86101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 34222 17.99 - 35.98: 3715 35.98 - 53.97: 673 53.97 - 71.96: 101 71.96 - 89.95: 42 Dihedral angle restraints: 38753 sinusoidal: 15553 harmonic: 23200 Sorted by residual: dihedral pdb=" C PHE X 310 " pdb=" N PHE X 310 " pdb=" CA PHE X 310 " pdb=" CB PHE X 310 " ideal model delta harmonic sigma weight residual -122.60 -141.16 18.56 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C TYR 4 81 " pdb=" N TYR 4 81 " pdb=" CA TYR 4 81 " pdb=" CB TYR 4 81 " ideal model delta harmonic sigma weight residual -122.60 -139.16 16.56 0 2.50e+00 1.60e-01 4.39e+01 dihedral pdb=" N PHE X 310 " pdb=" C PHE X 310 " pdb=" CA PHE X 310 " pdb=" CB PHE X 310 " ideal model delta harmonic sigma weight residual 122.80 138.14 -15.34 0 2.50e+00 1.60e-01 3.76e+01 ... (remaining 38750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 9356 0.138 - 0.276: 487 0.276 - 0.414: 28 0.414 - 0.552: 5 0.552 - 0.690: 2 Chirality restraints: 9878 Sorted by residual: chirality pdb=" CA PHE X 310 " pdb=" N PHE X 310 " pdb=" C PHE X 310 " pdb=" CB PHE X 310 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA TYR 4 81 " pdb=" N TYR 4 81 " pdb=" C TYR 4 81 " pdb=" CB TYR 4 81 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CA GLN T 204 " pdb=" N GLN T 204 " pdb=" C GLN T 204 " pdb=" CB GLN T 204 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 9875 not shown) Planarity restraints: 10995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG P 640 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO P 641 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO P 641 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 641 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 167 " -0.021 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" C ASN A 167 " 0.071 2.00e-02 2.50e+03 pdb=" O ASN A 167 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS A 168 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 975 " -0.061 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO X 976 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO X 976 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO X 976 " -0.050 5.00e-02 4.00e+02 ... (remaining 10992 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 8997 2.75 - 3.28: 60634 3.28 - 3.82: 103968 3.82 - 4.36: 120686 4.36 - 4.90: 207535 Nonbonded interactions: 501820 Sorted by model distance: nonbonded pdb=" O GLU Y 45 " pdb=" O ASN Y 48 " model vdw 2.207 3.040 nonbonded pdb=" O ASN W 726 " pdb=" OG SER W 873 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR W 764 " pdb=" OE2 GLU W 799 " model vdw 2.216 2.440 nonbonded pdb=" O GLY H 54 " pdb=" OG1 THR H 58 " model vdw 2.218 2.440 nonbonded pdb=" CD1 ILE G 18 " pdb=" OH TYR 4 51 " model vdw 2.223 3.460 ... (remaining 501815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 26.630 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 136.490 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.230 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 0.106 63572 Z= 0.742 Angle : 1.171 13.260 86106 Z= 0.699 Chirality : 0.070 0.690 9878 Planarity : 0.009 0.105 10995 Dihedral : 15.265 89.949 23597 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.63 % Favored : 93.77 % Rotamer: Outliers : 1.08 % Allowed : 8.90 % Favored : 90.02 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.08), residues: 7758 helix: -1.08 (0.07), residues: 4210 sheet: -1.43 (0.16), residues: 842 loop : -2.81 (0.10), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP X 798 HIS 0.017 0.002 HIS Q 383 PHE 0.037 0.003 PHE N 152 TYR 0.026 0.003 TYR N 166 ARG 0.012 0.001 ARG P 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1441 time to evaluate : 5.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.1851 (mmp) cc_final: 0.1573 (ptm) REVERT: A 492 ASP cc_start: 0.7209 (m-30) cc_final: 0.6706 (m-30) REVERT: D 92 GLU cc_start: 0.4099 (tm-30) cc_final: 0.3412 (mt-10) REVERT: D 119 GLN cc_start: 0.4966 (tm-30) cc_final: 0.3485 (mt0) REVERT: F 174 ARG cc_start: 0.5630 (mmt180) cc_final: 0.4514 (ptt-90) REVERT: F 187 LYS cc_start: 0.6788 (ttmt) cc_final: 0.6527 (ttmm) REVERT: G 44 MET cc_start: 0.1000 (ttp) cc_final: -0.0562 (mpp) REVERT: G 70 MET cc_start: 0.3965 (mmm) cc_final: 0.3691 (mtt) REVERT: G 162 GLU cc_start: 0.2853 (pp20) cc_final: 0.2085 (tm-30) REVERT: I 76 MET cc_start: 0.3229 (tmm) cc_final: 0.2906 (mpp) REVERT: I 104 MET cc_start: 0.3190 (mmp) cc_final: 0.2598 (tmm) REVERT: I 121 LEU cc_start: 0.5137 (mt) cc_final: 0.4804 (tp) REVERT: K 114 MET cc_start: 0.8445 (ttt) cc_final: 0.8198 (ttp) REVERT: N 227 GLU cc_start: 0.6565 (mp0) cc_final: 0.6066 (mp0) REVERT: N 305 LEU cc_start: 0.8506 (mt) cc_final: 0.8031 (tt) REVERT: N 674 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7053 (tm-30) REVERT: N 703 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7526 (ttp-110) REVERT: N 795 ASN cc_start: 0.7713 (t0) cc_final: 0.7360 (t0) REVERT: N 799 GLU cc_start: 0.4879 (mm-30) cc_final: 0.4593 (mm-30) REVERT: N 841 ASN cc_start: 0.8175 (m-40) cc_final: 0.7935 (m-40) REVERT: N 870 GLN cc_start: 0.8315 (tp40) cc_final: 0.7589 (tt0) REVERT: N 924 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (mp) REVERT: N 1286 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8068 (tm-30) REVERT: O 750 GLN cc_start: 0.7335 (mt0) cc_final: 0.6987 (mm-40) REVERT: P 30 CYS cc_start: 0.8779 (t) cc_final: 0.8384 (m) REVERT: P 90 ASP cc_start: 0.7759 (t0) cc_final: 0.7345 (t70) REVERT: P 163 LYS cc_start: 0.8475 (tptt) cc_final: 0.8071 (tptt) REVERT: P 369 LYS cc_start: 0.7934 (mttt) cc_final: 0.7640 (tppt) REVERT: P 447 ASP cc_start: 0.8132 (m-30) cc_final: 0.7853 (m-30) REVERT: P 471 LEU cc_start: 0.8006 (mm) cc_final: 0.7796 (mt) REVERT: P 472 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7833 (mtp180) REVERT: P 598 ASN cc_start: 0.8146 (m-40) cc_final: 0.7639 (t0) REVERT: P 754 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8198 (tpt170) REVERT: P 825 LYS cc_start: 0.8685 (pttt) cc_final: 0.8402 (ptmt) REVERT: Q 250 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (p0) REVERT: Q 264 GLN cc_start: 0.6200 (tm-30) cc_final: 0.5773 (mp10) REVERT: Q 328 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7223 (pttt) REVERT: Q 643 MET cc_start: 0.9182 (mtt) cc_final: 0.8876 (mtt) REVERT: R 32 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3665 (tp) REVERT: R 93 MET cc_start: 0.3140 (mmt) cc_final: 0.2784 (ptt) REVERT: R 119 MET cc_start: 0.7726 (mmm) cc_final: 0.7147 (ptt) REVERT: R 143 ILE cc_start: 0.6822 (mm) cc_final: 0.6368 (mt) REVERT: R 201 LYS cc_start: 0.5681 (ttpt) cc_final: 0.4731 (pptt) REVERT: T 1 MET cc_start: 0.6773 (ptp) cc_final: 0.6107 (ptp) REVERT: T 119 TYR cc_start: 0.8199 (t80) cc_final: 0.7997 (t80) REVERT: T 121 ASP cc_start: 0.7918 (m-30) cc_final: 0.7674 (m-30) REVERT: T 152 ASP cc_start: 0.7112 (m-30) cc_final: 0.6332 (t0) REVERT: V 98 ILE cc_start: 0.6003 (mt) cc_final: 0.5686 (mm) REVERT: V 103 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7729 (tm-30) REVERT: V 108 LEU cc_start: 0.8525 (tp) cc_final: 0.7897 (tp) REVERT: V 126 ASP cc_start: 0.7774 (m-30) cc_final: 0.7249 (m-30) REVERT: W 37 LEU cc_start: 0.8452 (mt) cc_final: 0.8190 (mt) REVERT: W 111 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7980 (mtp180) REVERT: W 282 MET cc_start: 0.8333 (ttt) cc_final: 0.8017 (ttt) REVERT: W 310 TYR cc_start: 0.8533 (t80) cc_final: 0.8166 (t80) REVERT: W 338 LEU cc_start: 0.9242 (tp) cc_final: 0.8912 (tt) REVERT: W 354 LEU cc_start: 0.9025 (pp) cc_final: 0.8776 (pp) REVERT: W 396 MET cc_start: 0.8751 (mtt) cc_final: 0.8273 (mtp) REVERT: W 498 THR cc_start: 0.7721 (p) cc_final: 0.7393 (t) REVERT: W 646 GLU cc_start: 0.7550 (tt0) cc_final: 0.7300 (tm-30) REVERT: W 672 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7738 (Cg_exo) REVERT: W 796 MET cc_start: 0.7961 (mtt) cc_final: 0.7531 (ttt) REVERT: W 811 LEU cc_start: 0.8242 (mt) cc_final: 0.7740 (mt) REVERT: W 1012 TYR cc_start: 0.8907 (m-80) cc_final: 0.8621 (m-80) REVERT: W 1277 MET cc_start: 0.8921 (mtt) cc_final: 0.8425 (mtp) REVERT: X 29 LYS cc_start: 0.8479 (mttt) cc_final: 0.7992 (ttpt) REVERT: X 183 LEU cc_start: 0.6786 (mp) cc_final: 0.6349 (tt) REVERT: X 222 ILE cc_start: 0.7186 (mt) cc_final: 0.6911 (mt) REVERT: X 223 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7548 (mmm160) REVERT: X 273 MET cc_start: 0.8429 (mmt) cc_final: 0.8053 (mtp) REVERT: X 604 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7968 (tttm) REVERT: X 654 ASN cc_start: 0.7087 (m-40) cc_final: 0.6745 (t0) REVERT: X 837 ARG cc_start: 0.6721 (mtt180) cc_final: 0.6422 (ttm-80) REVERT: X 894 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7802 (mtp-110) REVERT: Y 195 PHE cc_start: 0.7782 (t80) cc_final: 0.7423 (t80) REVERT: Y 220 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (ttm) REVERT: Y 224 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7312 (mtt90) REVERT: 0 109 GLN cc_start: 0.7271 (tp40) cc_final: 0.7029 (tt0) REVERT: 0 160 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7446 (tm-30) REVERT: 0 164 ASP cc_start: 0.7165 (m-30) cc_final: 0.6165 (m-30) REVERT: 0 229 ASP cc_start: 0.8997 (t0) cc_final: 0.8779 (t70) REVERT: 0 287 PHE cc_start: 0.8277 (m-80) cc_final: 0.7807 (m-80) REVERT: 0 307 ASP cc_start: 0.8325 (p0) cc_final: 0.7738 (t0) REVERT: 1 103 SER cc_start: 0.8948 (t) cc_final: 0.8705 (m) REVERT: 1 121 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7804 (mm-30) REVERT: 1 131 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8458 (ttmm) REVERT: 2 80 GLN cc_start: 0.8242 (mt0) cc_final: 0.7981 (mt0) REVERT: 2 89 ASP cc_start: 0.7918 (m-30) cc_final: 0.7686 (m-30) REVERT: 2 117 GLU cc_start: 0.8416 (tt0) cc_final: 0.8188 (tt0) REVERT: 3 46 TYR cc_start: 0.7643 (t80) cc_final: 0.7125 (t80) REVERT: 4 75 MET cc_start: 0.0932 (mmm) cc_final: -0.0160 (mtm) REVERT: 4 80 GLN cc_start: 0.2203 (OUTLIER) cc_final: 0.1734 (tp40) REVERT: 4 113 MET cc_start: 0.1876 (mmm) cc_final: 0.0817 (ptm) outliers start: 74 outliers final: 20 residues processed: 1497 average time/residue: 0.6223 time to fit residues: 1526.8116 Evaluate side-chains 766 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 740 time to evaluate : 5.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 PHE Chi-restraints excluded: chain I residue 105 PRO Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 725 VAL Chi-restraints excluded: chain N residue 924 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain Y residue 220 MET Chi-restraints excluded: chain Y residue 224 ARG Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 218 ASN Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 659 optimal weight: 2.9990 chunk 591 optimal weight: 2.9990 chunk 328 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 399 optimal weight: 4.9990 chunk 316 optimal weight: 0.6980 chunk 612 optimal weight: 0.9980 chunk 236 optimal weight: 0.0370 chunk 372 optimal weight: 0.9980 chunk 455 optimal weight: 0.9980 chunk 709 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 322 GLN A 359 HIS A 400 HIS A 413 HIS A 414 GLN A 439 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN F 46 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN G 142 GLN H 7 GLN H 18 GLN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN K 77 GLN K 113 GLN N 267 HIS N 309 HIS N 521 GLN N 532 ASN N 590 GLN N 638 ASN N 669 GLN N 849 ASN N 856 GLN N 964 ASN N1179 HIS O 679 GLN ** O 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 746 ASN P 63 HIS P 80 HIS P 113 HIS P 272 ASN P 282 HIS P 435 GLN ** P 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 619 GLN P 634 ASN P 751 GLN Q 100 ASN Q 139 GLN Q 193 HIS Q 219 HIS Q 340 GLN Q 468 ASN Q 492 GLN Q 506 HIS Q 517 GLN Q 532 HIS Q 539 GLN Q 565 ASN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 GLN T 103 GLN T 162 GLN T 192 GLN ** T 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN U 56 GLN U 119 GLN V 32 ASN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 293 HIS W 337 GLN W 357 HIS W 378 GLN W 513 ASN ** W 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 844 ASN W 851 ASN W 921 HIS W 923 ASN W 925 HIS W 972 HIS W 990 HIS W1059 ASN W1198 GLN W1261 GLN W1300 HIS W1320 ASN X 8 GLN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 179 HIS X 217 GLN X 266 GLN X 361 ASN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 402 ASN ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 472 ASN X 502 HIS X 544 HIS X 627 HIS X 641 GLN ** X 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 218 ASN 0 306 HIS 1 130 GLN ** 1 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 167 GLN 2 175 HIS 2 183 ASN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63572 Z= 0.232 Angle : 0.679 13.930 86106 Z= 0.348 Chirality : 0.043 0.259 9878 Planarity : 0.005 0.082 10995 Dihedral : 6.096 79.397 8475 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.70 % Rotamer: Outliers : 2.76 % Allowed : 14.36 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 7758 helix: 0.75 (0.08), residues: 4280 sheet: -1.06 (0.16), residues: 848 loop : -2.38 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 4 105 HIS 0.009 0.001 HIS N 201 PHE 0.030 0.002 PHE F 172 TYR 0.027 0.002 TYR A 210 ARG 0.011 0.001 ARG Z 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 847 time to evaluate : 5.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.1963 (mmp) cc_final: 0.1637 (ptp) REVERT: A 361 MET cc_start: 0.7384 (mmm) cc_final: 0.6861 (mtm) REVERT: A 477 CYS cc_start: 0.2648 (m) cc_final: 0.1563 (m) REVERT: D 92 GLU cc_start: 0.3787 (tm-30) cc_final: 0.3431 (mt-10) REVERT: D 182 MET cc_start: 0.1962 (OUTLIER) cc_final: 0.1555 (mmp) REVERT: G 44 MET cc_start: 0.1357 (ttp) cc_final: -0.0238 (mmp) REVERT: G 114 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.4968 (mt) REVERT: G 139 MET cc_start: 0.0169 (mmp) cc_final: -0.0076 (mmp) REVERT: I 76 MET cc_start: 0.3522 (tmm) cc_final: 0.3265 (mpp) REVERT: I 104 MET cc_start: 0.3384 (mmp) cc_final: 0.2407 (tpt) REVERT: K 20 GLU cc_start: 0.2063 (OUTLIER) cc_final: 0.1802 (pt0) REVERT: K 92 MET cc_start: 0.7735 (mmt) cc_final: 0.7414 (mmt) REVERT: N 117 MET cc_start: -0.0084 (tmm) cc_final: -0.0304 (ptm) REVERT: N 227 GLU cc_start: 0.6645 (mp0) cc_final: 0.6271 (mp0) REVERT: N 305 LEU cc_start: 0.8290 (mt) cc_final: 0.7866 (tt) REVERT: N 450 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7231 (mt-10) REVERT: N 674 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7081 (tm-30) REVERT: N 703 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7496 (ttp-110) REVERT: N 795 ASN cc_start: 0.7858 (t0) cc_final: 0.7562 (t0) REVERT: N 870 GLN cc_start: 0.8216 (tp40) cc_final: 0.7597 (tt0) REVERT: O 681 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7508 (mt-10) REVERT: O 714 ASP cc_start: 0.7655 (m-30) cc_final: 0.7220 (t0) REVERT: P 13 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6469 (mmm) REVERT: P 30 CYS cc_start: 0.8628 (t) cc_final: 0.8333 (m) REVERT: P 163 LYS cc_start: 0.8443 (tptt) cc_final: 0.8038 (tptt) REVERT: P 198 GLN cc_start: 0.7970 (tt0) cc_final: 0.7762 (tt0) REVERT: P 382 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8545 (mt) REVERT: P 472 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7912 (mtp180) REVERT: P 598 ASN cc_start: 0.8082 (m-40) cc_final: 0.7600 (t0) REVERT: P 645 PHE cc_start: 0.8812 (m-80) cc_final: 0.8494 (m-80) REVERT: P 745 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8057 (tppt) REVERT: P 754 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.8002 (tpt170) REVERT: Q 264 GLN cc_start: 0.5961 (tm-30) cc_final: 0.5536 (mp10) REVERT: Q 392 MET cc_start: 0.6351 (tpp) cc_final: 0.6143 (tpp) REVERT: Q 643 MET cc_start: 0.9116 (mtt) cc_final: 0.8888 (mtt) REVERT: R 32 LEU cc_start: 0.3347 (OUTLIER) cc_final: 0.3140 (tp) REVERT: R 119 MET cc_start: 0.7639 (mmm) cc_final: 0.7087 (ptt) REVERT: R 121 MET cc_start: 0.4928 (mmm) cc_final: 0.4629 (mtt) REVERT: R 191 GLU cc_start: 0.7452 (pt0) cc_final: 0.7157 (mm-30) REVERT: R 201 LYS cc_start: 0.5822 (ttpt) cc_final: 0.4606 (pptt) REVERT: T 1 MET cc_start: 0.6638 (ptp) cc_final: 0.6111 (ptp) REVERT: T 71 TYR cc_start: 0.7846 (m-80) cc_final: 0.7609 (m-80) REVERT: T 81 ASN cc_start: 0.7781 (t0) cc_final: 0.7342 (t0) REVERT: T 165 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7741 (mp) REVERT: T 194 MET cc_start: 0.7232 (tmm) cc_final: 0.6945 (ptm) REVERT: U 61 LEU cc_start: 0.2338 (tp) cc_final: 0.1066 (pp) REVERT: V 78 LEU cc_start: 0.5431 (tt) cc_final: 0.5070 (mm) REVERT: V 106 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7122 (ttm170) REVERT: W 37 LEU cc_start: 0.8383 (mt) cc_final: 0.8157 (mt) REVERT: W 230 VAL cc_start: 0.9590 (t) cc_final: 0.9321 (m) REVERT: W 293 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.6277 (t-170) REVERT: W 310 TYR cc_start: 0.8535 (t80) cc_final: 0.8321 (t80) REVERT: W 373 MET cc_start: 0.8661 (mmm) cc_final: 0.8336 (mmm) REVERT: W 660 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: W 770 MET cc_start: 0.3300 (ttt) cc_final: 0.2976 (ptm) REVERT: W 782 MET cc_start: 0.4697 (ptt) cc_final: 0.4376 (ptp) REVERT: W 1011 TYR cc_start: 0.8597 (t80) cc_final: 0.8279 (t80) REVERT: W 1012 TYR cc_start: 0.8776 (m-80) cc_final: 0.8521 (m-80) REVERT: W 1277 MET cc_start: 0.8767 (mtt) cc_final: 0.8231 (mtp) REVERT: X 29 LYS cc_start: 0.8330 (mttt) cc_final: 0.7837 (tttt) REVERT: X 223 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7555 (mmm160) REVERT: X 269 MET cc_start: 0.7951 (tpp) cc_final: 0.7668 (tpp) REVERT: X 301 GLU cc_start: 0.7767 (mp0) cc_final: 0.7428 (mp0) REVERT: X 366 GLU cc_start: 0.7357 (tp30) cc_final: 0.7110 (mm-30) REVERT: X 382 MET cc_start: 0.8636 (mtp) cc_final: 0.8373 (mtp) REVERT: X 630 MET cc_start: 0.8584 (mmm) cc_final: 0.8256 (mmm) REVERT: X 654 ASN cc_start: 0.6980 (m-40) cc_final: 0.6655 (t0) REVERT: Y 109 GLU cc_start: 0.6568 (pm20) cc_final: 0.6275 (pm20) REVERT: Y 195 PHE cc_start: 0.7890 (t80) cc_final: 0.7299 (t80) REVERT: Y 213 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8345 (t) REVERT: Y 224 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7191 (mtt90) REVERT: Z 482 ARG cc_start: 0.1043 (OUTLIER) cc_final: -0.0336 (tpp80) REVERT: 0 73 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7976 (mp) REVERT: 0 287 PHE cc_start: 0.8360 (m-80) cc_final: 0.7857 (m-80) REVERT: 1 86 ASP cc_start: 0.8681 (t0) cc_final: 0.8354 (m-30) REVERT: 1 103 SER cc_start: 0.9021 (t) cc_final: 0.8701 (m) REVERT: 2 80 GLN cc_start: 0.8216 (mt0) cc_final: 0.7968 (mt0) REVERT: 3 173 MET cc_start: 0.9180 (mtm) cc_final: 0.8928 (mtm) REVERT: 4 75 MET cc_start: 0.0678 (mmm) cc_final: -0.0359 (mtm) REVERT: 4 80 GLN cc_start: 0.2231 (OUTLIER) cc_final: 0.1776 (tp40) REVERT: 4 113 MET cc_start: 0.2234 (mmm) cc_final: 0.0539 (ptm) outliers start: 189 outliers final: 87 residues processed: 989 average time/residue: 0.5666 time to fit residues: 958.8640 Evaluate side-chains 766 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 665 time to evaluate : 5.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 20 GLU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 933 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 735 LEU Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 648 ASP Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 730 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 147 CYS Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 293 HIS Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 585 ILE Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 970 VAL Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1262 GLU Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 529 MET Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 943 VAL Chi-restraints excluded: chain X residue 954 GLU Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 213 VAL Chi-restraints excluded: chain Y residue 224 ARG Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 73 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 177 SER Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 1 residue 78 ASP Chi-restraints excluded: chain 1 residue 146 ILE Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 394 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 590 optimal weight: 2.9990 chunk 482 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 710 optimal weight: 0.8980 chunk 767 optimal weight: 0.8980 chunk 632 optimal weight: 3.9990 chunk 704 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 569 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 825 ASN N 849 ASN O 697 HIS ** O 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 375 GLN P 598 ASN Q 193 HIS Q 219 HIS Q 528 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 611 GLN Q 626 GLN T 103 GLN ** T 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 205 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN V 89 ASN W 4 GLN ** W 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 293 HIS W 628 HIS W 717 GLN W 783 GLN ** W 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN W1250 HIS X 12 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 483 ASN Z 556 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 75 ASN 1 109 GLN 1 132 HIS 2 183 ASN 3 53 GLN 3 59 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 63572 Z= 0.308 Angle : 0.670 12.266 86106 Z= 0.342 Chirality : 0.043 0.241 9878 Planarity : 0.005 0.079 10995 Dihedral : 5.603 83.199 8457 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 3.68 % Allowed : 16.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.09), residues: 7758 helix: 1.38 (0.08), residues: 4288 sheet: -0.86 (0.17), residues: 858 loop : -2.20 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP W1183 HIS 0.023 0.001 HIS W 293 PHE 0.021 0.002 PHE X 468 TYR 0.023 0.002 TYR W 832 ARG 0.015 0.001 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 709 time to evaluate : 6.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.2060 (mmp) cc_final: 0.1444 (ptt) REVERT: A 231 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5212 (tp) REVERT: A 361 MET cc_start: 0.7561 (mmm) cc_final: 0.6935 (mtm) REVERT: D 72 ARG cc_start: 0.4797 (mmm-85) cc_final: 0.4491 (tpp-160) REVERT: D 182 MET cc_start: 0.2262 (OUTLIER) cc_final: 0.1818 (mmp) REVERT: F 174 ARG cc_start: 0.5272 (mmt180) cc_final: 0.4357 (ptt-90) REVERT: G 43 MET cc_start: -0.1324 (tmm) cc_final: -0.2565 (pmm) REVERT: G 44 MET cc_start: 0.1458 (ttp) cc_final: -0.0283 (mmp) REVERT: G 114 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5008 (mt) REVERT: G 138 MET cc_start: 0.1613 (mtp) cc_final: -0.0007 (tpt) REVERT: G 162 GLU cc_start: 0.3538 (pp20) cc_final: 0.2716 (tp30) REVERT: H 158 GLU cc_start: 0.2267 (pp20) cc_final: 0.1200 (mm-30) REVERT: I 88 ASN cc_start: 0.2443 (OUTLIER) cc_final: 0.0704 (t0) REVERT: I 104 MET cc_start: 0.3018 (mmp) cc_final: 0.2766 (tmm) REVERT: K 57 GLN cc_start: 0.5559 (tp40) cc_final: 0.4895 (tt0) REVERT: N 117 MET cc_start: 0.0009 (tmm) cc_final: -0.0251 (ptm) REVERT: N 305 LEU cc_start: 0.8384 (mt) cc_final: 0.7959 (tt) REVERT: N 458 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8039 (pp) REVERT: N 674 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7414 (tm-30) REVERT: N 703 ARG cc_start: 0.7799 (ptp90) cc_final: 0.7522 (ttp-110) REVERT: N 795 ASN cc_start: 0.7884 (t0) cc_final: 0.7654 (t0) REVERT: N 849 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8224 (t0) REVERT: O 714 ASP cc_start: 0.7836 (m-30) cc_final: 0.7385 (t0) REVERT: O 766 LYS cc_start: 0.8532 (mttt) cc_final: 0.8274 (mmtp) REVERT: P 30 CYS cc_start: 0.8553 (t) cc_final: 0.8251 (m) REVERT: P 51 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7737 (mp) REVERT: P 198 GLN cc_start: 0.7947 (tt0) cc_final: 0.7744 (tt0) REVERT: P 382 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8545 (mt) REVERT: P 472 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7631 (tmt170) REVERT: P 598 ASN cc_start: 0.8328 (m110) cc_final: 0.7334 (t0) REVERT: P 645 PHE cc_start: 0.8822 (m-80) cc_final: 0.8580 (m-80) REVERT: P 745 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8067 (tppt) REVERT: Q 264 GLN cc_start: 0.6054 (tm-30) cc_final: 0.5523 (mp10) REVERT: R 32 LEU cc_start: 0.3416 (OUTLIER) cc_final: 0.3162 (tp) REVERT: R 119 MET cc_start: 0.7643 (mmm) cc_final: 0.7116 (ptt) REVERT: R 191 GLU cc_start: 0.7364 (pt0) cc_final: 0.6937 (mm-30) REVERT: R 201 LYS cc_start: 0.5994 (ttpt) cc_final: 0.4636 (pptt) REVERT: T 1 MET cc_start: 0.6633 (ptp) cc_final: 0.6122 (ptp) REVERT: T 71 TYR cc_start: 0.7933 (m-80) cc_final: 0.7507 (m-80) REVERT: T 81 ASN cc_start: 0.7752 (t0) cc_final: 0.7234 (t0) REVERT: T 152 ASP cc_start: 0.6961 (m-30) cc_final: 0.6008 (t0) REVERT: T 153 CYS cc_start: 0.8065 (p) cc_final: 0.7675 (p) REVERT: T 194 MET cc_start: 0.7339 (tmm) cc_final: 0.6874 (ptm) REVERT: U 61 LEU cc_start: 0.2327 (tp) cc_final: 0.1032 (pp) REVERT: V 78 LEU cc_start: 0.5381 (tt) cc_final: 0.4937 (mm) REVERT: W 37 LEU cc_start: 0.8449 (mt) cc_final: 0.8184 (mt) REVERT: W 310 TYR cc_start: 0.8503 (t80) cc_final: 0.8291 (t80) REVERT: W 342 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8858 (p) REVERT: W 373 MET cc_start: 0.8647 (mmm) cc_final: 0.8282 (mmm) REVERT: W 495 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6635 (pt) REVERT: W 782 MET cc_start: 0.5068 (ptt) cc_final: 0.4759 (ptp) REVERT: W 1014 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7675 (tmm) REVERT: W 1277 MET cc_start: 0.8802 (mtt) cc_final: 0.8481 (mtp) REVERT: X 223 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7541 (mmm160) REVERT: X 269 MET cc_start: 0.8005 (tpp) cc_final: 0.7612 (tpp) REVERT: X 301 GLU cc_start: 0.7833 (mp0) cc_final: 0.7496 (mp0) REVERT: X 366 GLU cc_start: 0.7429 (tp30) cc_final: 0.7155 (mm-30) REVERT: X 499 MET cc_start: 0.7746 (mtp) cc_final: 0.7359 (mtp) REVERT: X 654 ASN cc_start: 0.7095 (m-40) cc_final: 0.6782 (t0) REVERT: Y 227 VAL cc_start: 0.8968 (t) cc_final: 0.8606 (m) REVERT: Z 482 ARG cc_start: 0.0612 (OUTLIER) cc_final: -0.0628 (tpp80) REVERT: 0 69 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7631 (tm-30) REVERT: 0 267 MET cc_start: 0.9067 (mmm) cc_final: 0.8854 (mmt) REVERT: 0 287 PHE cc_start: 0.8392 (m-80) cc_final: 0.7954 (m-80) REVERT: 1 49 GLU cc_start: 0.8159 (tt0) cc_final: 0.7906 (tt0) REVERT: 1 86 ASP cc_start: 0.8729 (t0) cc_final: 0.8357 (m-30) REVERT: 1 103 SER cc_start: 0.9030 (t) cc_final: 0.8711 (m) REVERT: 2 183 ASN cc_start: 0.7737 (m-40) cc_final: 0.6850 (t0) REVERT: 2 186 THR cc_start: 0.5193 (OUTLIER) cc_final: 0.4846 (p) REVERT: 3 173 MET cc_start: 0.9165 (mtm) cc_final: 0.8938 (mtm) REVERT: 4 75 MET cc_start: 0.1051 (mmm) cc_final: -0.0078 (mtt) REVERT: 4 80 GLN cc_start: 0.3011 (OUTLIER) cc_final: 0.2080 (tp40) REVERT: 4 105 TRP cc_start: 0.1408 (t60) cc_final: 0.1157 (t60) outliers start: 252 outliers final: 129 residues processed: 902 average time/residue: 0.5512 time to fit residues: 857.0254 Evaluate side-chains 770 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 626 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 849 ASN Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 933 VAL Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 674 ILE Chi-restraints excluded: chain O residue 718 VAL Chi-restraints excluded: chain O residue 735 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 443 LEU Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 714 VAL Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 334 LEU Chi-restraints excluded: chain W residue 342 VAL Chi-restraints excluded: chain W residue 352 MET Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1262 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 0 residue 301 THR Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 701 optimal weight: 0.8980 chunk 534 optimal weight: 0.2980 chunk 368 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 339 optimal weight: 0.9980 chunk 477 optimal weight: 0.9980 chunk 713 optimal weight: 0.9990 chunk 754 optimal weight: 0.9980 chunk 372 optimal weight: 0.9990 chunk 675 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 ASN O 697 HIS O 701 ASN O 742 GLN ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN T 162 GLN ** T 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN W 4 GLN ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 63572 Z= 0.190 Angle : 0.591 11.156 86106 Z= 0.300 Chirality : 0.041 0.198 9878 Planarity : 0.004 0.074 10995 Dihedral : 5.154 85.359 8445 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 3.20 % Allowed : 17.15 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 7758 helix: 1.83 (0.08), residues: 4293 sheet: -0.70 (0.17), residues: 845 loop : -2.07 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 105 HIS 0.008 0.001 HIS K 58 PHE 0.021 0.001 PHE Y 195 TYR 0.021 0.001 TYR W 832 ARG 0.009 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 701 time to evaluate : 5.755 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: A 65 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4560 (mm) REVERT: A 77 MET cc_start: 0.1633 (mmp) cc_final: 0.1074 (ptt) REVERT: A 231 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.5253 (tp) REVERT: A 270 ILE cc_start: 0.0690 (OUTLIER) cc_final: 0.0305 (mt) REVERT: A 361 MET cc_start: 0.7627 (mmm) cc_final: 0.7038 (mtm) REVERT: D 72 ARG cc_start: 0.4667 (mmm-85) cc_final: 0.4422 (tpp-160) REVERT: D 182 MET cc_start: 0.2014 (OUTLIER) cc_final: 0.1727 (mmp) REVERT: F 174 ARG cc_start: 0.5167 (mmt180) cc_final: 0.4323 (ptt-90) REVERT: G 43 MET cc_start: -0.0809 (tmm) cc_final: -0.2749 (pmm) REVERT: G 44 MET cc_start: 0.1194 (ttp) cc_final: 0.0144 (mmp) REVERT: G 114 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.4993 (mt) REVERT: G 138 MET cc_start: 0.1417 (mtp) cc_final: -0.0044 (tpt) REVERT: G 162 GLU cc_start: 0.3462 (pp20) cc_final: 0.2711 (tp30) REVERT: H 158 GLU cc_start: 0.2296 (pp20) cc_final: 0.1267 (mm-30) REVERT: I 88 ASN cc_start: 0.2593 (OUTLIER) cc_final: 0.0794 (t0) REVERT: J 121 MET cc_start: -0.2466 (tpt) cc_final: -0.4199 (ptt) REVERT: K 57 GLN cc_start: 0.5451 (tp40) cc_final: 0.4799 (tt0) REVERT: K 77 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6388 (mm110) REVERT: K 92 MET cc_start: 0.7695 (mmt) cc_final: 0.7222 (mmt) REVERT: N 117 MET cc_start: -0.0028 (tmm) cc_final: -0.0327 (ptm) REVERT: N 299 PHE cc_start: 0.7609 (t80) cc_final: 0.7358 (t80) REVERT: N 305 LEU cc_start: 0.8354 (mt) cc_final: 0.7948 (tt) REVERT: N 375 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.5161 (p0) REVERT: N 450 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7251 (mt-10) REVERT: N 458 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8058 (pp) REVERT: N 547 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: N 674 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7326 (tm-30) REVERT: N 703 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7538 (ttp-110) REVERT: N 795 ASN cc_start: 0.7880 (t0) cc_final: 0.7675 (t0) REVERT: O 714 ASP cc_start: 0.7856 (m-30) cc_final: 0.7358 (t0) REVERT: O 766 LYS cc_start: 0.8547 (mttt) cc_final: 0.8299 (mmtp) REVERT: P 51 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7777 (mp) REVERT: P 382 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8502 (mt) REVERT: P 472 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7937 (mtp180) REVERT: P 598 ASN cc_start: 0.8340 (m110) cc_final: 0.7420 (t0) REVERT: P 645 PHE cc_start: 0.8731 (m-80) cc_final: 0.8405 (m-80) REVERT: P 745 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8042 (tppt) REVERT: P 754 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7794 (tpt170) REVERT: Q 264 GLN cc_start: 0.6073 (tm-30) cc_final: 0.5572 (mp10) REVERT: Q 478 LEU cc_start: 0.8456 (mp) cc_final: 0.8038 (tt) REVERT: R 32 LEU cc_start: 0.3334 (OUTLIER) cc_final: 0.3033 (tp) REVERT: R 119 MET cc_start: 0.7646 (mmm) cc_final: 0.7120 (ptt) REVERT: R 191 GLU cc_start: 0.7383 (pt0) cc_final: 0.6977 (mm-30) REVERT: R 193 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5647 (pp) REVERT: R 201 LYS cc_start: 0.5992 (ttpt) cc_final: 0.4609 (pptt) REVERT: T 1 MET cc_start: 0.6595 (ptp) cc_final: 0.6048 (ptp) REVERT: T 81 ASN cc_start: 0.7760 (t0) cc_final: 0.7231 (t0) REVERT: T 153 CYS cc_start: 0.8125 (p) cc_final: 0.7777 (p) REVERT: T 194 MET cc_start: 0.7376 (tmm) cc_final: 0.6839 (ptm) REVERT: U 61 LEU cc_start: 0.2294 (tp) cc_final: 0.1017 (pp) REVERT: V 78 LEU cc_start: 0.5267 (tt) cc_final: 0.4926 (mm) REVERT: W 37 LEU cc_start: 0.8416 (mt) cc_final: 0.8152 (mt) REVERT: W 230 VAL cc_start: 0.9552 (t) cc_final: 0.9327 (m) REVERT: W 310 TYR cc_start: 0.8486 (t80) cc_final: 0.8286 (t80) REVERT: W 343 LEU cc_start: 0.8493 (tt) cc_final: 0.8203 (mp) REVERT: W 373 MET cc_start: 0.8691 (mmm) cc_final: 0.8312 (mmm) REVERT: W 495 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6647 (pt) REVERT: W 796 MET cc_start: 0.7684 (mtt) cc_final: 0.7212 (ttt) REVERT: W 976 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7579 (mt-10) REVERT: W 1012 TYR cc_start: 0.8764 (m-80) cc_final: 0.8446 (m-80) REVERT: W 1014 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: W 1265 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7301 (mtm110) REVERT: W 1277 MET cc_start: 0.8752 (mtt) cc_final: 0.8436 (mtp) REVERT: X 223 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7574 (mmm160) REVERT: X 301 GLU cc_start: 0.7793 (mp0) cc_final: 0.7422 (mp0) REVERT: X 366 GLU cc_start: 0.7356 (tp30) cc_final: 0.7095 (mm-30) REVERT: X 499 MET cc_start: 0.7670 (mtp) cc_final: 0.7234 (mtp) REVERT: X 654 ASN cc_start: 0.6890 (m-40) cc_final: 0.6615 (t0) REVERT: X 676 ASP cc_start: 0.7744 (p0) cc_final: 0.7530 (p0) REVERT: X 897 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7812 (tt) REVERT: Y 227 VAL cc_start: 0.9007 (t) cc_final: 0.8660 (m) REVERT: Z 482 ARG cc_start: 0.0635 (OUTLIER) cc_final: -0.0718 (tpp80) REVERT: 0 69 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7373 (tm-30) REVERT: 0 287 PHE cc_start: 0.8333 (m-80) cc_final: 0.7940 (m-80) REVERT: 0 303 GLU cc_start: 0.7860 (mp0) cc_final: 0.7453 (pm20) REVERT: 1 86 ASP cc_start: 0.8730 (t0) cc_final: 0.8350 (m-30) REVERT: 1 103 SER cc_start: 0.9026 (t) cc_final: 0.8738 (m) REVERT: 2 80 GLN cc_start: 0.8289 (mt0) cc_final: 0.8037 (mt0) REVERT: 2 183 ASN cc_start: 0.7833 (m-40) cc_final: 0.6750 (t0) REVERT: 2 186 THR cc_start: 0.5247 (OUTLIER) cc_final: 0.4916 (p) REVERT: 3 173 MET cc_start: 0.9163 (mtm) cc_final: 0.8954 (mtm) REVERT: 4 75 MET cc_start: 0.0519 (mmm) cc_final: -0.0098 (mtp) REVERT: 4 80 GLN cc_start: 0.3062 (OUTLIER) cc_final: 0.2081 (tp40) outliers start: 219 outliers final: 119 residues processed: 871 average time/residue: 0.5741 time to fit residues: 859.3520 Evaluate side-chains 781 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 641 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 621 LEU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 490 ASP Chi-restraints excluded: chain P residue 563 LEU Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 730 ASP Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 517 GLN Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 85 MET Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 897 LEU Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 166 THR Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 207 LEU Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 628 optimal weight: 0.9990 chunk 428 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 562 optimal weight: 0.5980 chunk 311 optimal weight: 2.9990 chunk 644 optimal weight: 0.8980 chunk 521 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 385 optimal weight: 1.9990 chunk 677 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN N 374 HIS O 697 HIS O 750 GLN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN Q 219 HIS Q 310 GLN Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN T 180 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN V 89 ASN W 898 ASN W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 832 GLN ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 19 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63572 Z= 0.187 Angle : 0.580 11.527 86106 Z= 0.292 Chirality : 0.040 0.217 9878 Planarity : 0.004 0.064 10995 Dihedral : 4.949 86.706 8441 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 3.58 % Allowed : 17.65 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.10), residues: 7758 helix: 2.07 (0.08), residues: 4295 sheet: -0.58 (0.17), residues: 847 loop : -1.96 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 105 HIS 0.009 0.001 HIS Q 219 PHE 0.021 0.001 PHE Y 195 TYR 0.018 0.001 TYR W 832 ARG 0.007 0.000 ARG 1 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 687 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4331 (pp) REVERT: A 77 MET cc_start: 0.1701 (mmp) cc_final: 0.1109 (ptt) REVERT: A 231 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5321 (tp) REVERT: A 270 ILE cc_start: 0.0800 (OUTLIER) cc_final: 0.0414 (mt) REVERT: A 361 MET cc_start: 0.7555 (mmm) cc_final: 0.7097 (mtm) REVERT: D 66 LEU cc_start: 0.3362 (OUTLIER) cc_final: 0.2935 (mp) REVERT: D 182 MET cc_start: 0.2008 (OUTLIER) cc_final: 0.1711 (mmp) REVERT: F 174 ARG cc_start: 0.5339 (mmt180) cc_final: 0.4449 (ptt-90) REVERT: G 43 MET cc_start: -0.1525 (tmm) cc_final: -0.2275 (pmm) REVERT: G 44 MET cc_start: 0.1264 (ttp) cc_final: 0.0159 (mmt) REVERT: G 114 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5117 (mt) REVERT: G 138 MET cc_start: 0.1097 (mtp) cc_final: 0.0134 (tpt) REVERT: H 158 GLU cc_start: 0.2208 (pp20) cc_final: 0.0984 (mm-30) REVERT: I 88 ASN cc_start: 0.2936 (OUTLIER) cc_final: 0.1094 (t0) REVERT: I 104 MET cc_start: 0.3949 (tmm) cc_final: 0.3442 (tpt) REVERT: J 121 MET cc_start: -0.2475 (tpt) cc_final: -0.4237 (ptt) REVERT: K 57 GLN cc_start: 0.5332 (tp40) cc_final: 0.4766 (tt0) REVERT: K 77 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6595 (mm110) REVERT: K 92 MET cc_start: 0.7670 (mmt) cc_final: 0.7215 (mmt) REVERT: N 117 MET cc_start: -0.0092 (tmm) cc_final: -0.0480 (ptm) REVERT: N 299 PHE cc_start: 0.7615 (t80) cc_final: 0.7385 (t80) REVERT: N 305 LEU cc_start: 0.8374 (mt) cc_final: 0.7986 (tt) REVERT: N 375 ASP cc_start: 0.5309 (OUTLIER) cc_final: 0.5048 (p0) REVERT: N 547 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: N 674 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7358 (tm-30) REVERT: N 691 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8645 (tptp) REVERT: N 703 ARG cc_start: 0.7859 (ptp90) cc_final: 0.7465 (ttp-110) REVERT: N 830 LYS cc_start: 0.7861 (mttt) cc_final: 0.7254 (mtmm) REVERT: O 714 ASP cc_start: 0.7904 (m-30) cc_final: 0.7387 (t0) REVERT: O 746 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: O 766 LYS cc_start: 0.8556 (mttt) cc_final: 0.8308 (mmtp) REVERT: P 51 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7800 (mp) REVERT: P 171 PHE cc_start: 0.8375 (t80) cc_final: 0.7936 (t80) REVERT: P 382 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8475 (mt) REVERT: P 472 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7941 (mtp180) REVERT: P 529 MET cc_start: 0.8376 (mtp) cc_final: 0.7952 (mtp) REVERT: P 598 ASN cc_start: 0.8299 (m110) cc_final: 0.7480 (t0) REVERT: P 645 PHE cc_start: 0.8727 (m-80) cc_final: 0.8349 (m-80) REVERT: P 745 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8006 (tppt) REVERT: P 754 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7817 (tpt170) REVERT: Q 95 TRP cc_start: 0.0953 (m-10) cc_final: 0.0739 (m-10) REVERT: Q 264 GLN cc_start: 0.6218 (tm-30) cc_final: 0.5589 (mp10) REVERT: Q 316 VAL cc_start: 0.8773 (t) cc_final: 0.8499 (m) REVERT: Q 478 LEU cc_start: 0.8448 (mp) cc_final: 0.8048 (tt) REVERT: Q 493 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8939 (mp) REVERT: R 32 LEU cc_start: 0.3389 (OUTLIER) cc_final: 0.3098 (tp) REVERT: R 119 MET cc_start: 0.7540 (mmm) cc_final: 0.7138 (ptt) REVERT: R 191 GLU cc_start: 0.7108 (pt0) cc_final: 0.6830 (mm-30) REVERT: R 201 LYS cc_start: 0.5873 (ttpt) cc_final: 0.4621 (pptt) REVERT: T 1 MET cc_start: 0.6484 (ptp) cc_final: 0.5914 (ptp) REVERT: T 63 MET cc_start: 0.4655 (ppp) cc_final: 0.3874 (ppp) REVERT: T 81 ASN cc_start: 0.7728 (t0) cc_final: 0.7217 (t0) REVERT: T 153 CYS cc_start: 0.8004 (p) cc_final: 0.7727 (p) REVERT: T 194 MET cc_start: 0.7479 (tmm) cc_final: 0.6916 (ptm) REVERT: T 204 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5926 (pp30) REVERT: U 61 LEU cc_start: 0.2276 (tp) cc_final: 0.0991 (pp) REVERT: V 78 LEU cc_start: 0.5245 (tt) cc_final: 0.4890 (mm) REVERT: W 4 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: W 37 LEU cc_start: 0.8438 (mt) cc_final: 0.8176 (mt) REVERT: W 230 VAL cc_start: 0.9543 (t) cc_final: 0.9310 (m) REVERT: W 310 TYR cc_start: 0.8473 (t80) cc_final: 0.8254 (t80) REVERT: W 343 LEU cc_start: 0.8579 (tt) cc_final: 0.8345 (mp) REVERT: W 373 MET cc_start: 0.8668 (mmm) cc_final: 0.8391 (mmm) REVERT: W 495 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6627 (pt) REVERT: W 796 MET cc_start: 0.7793 (mtt) cc_final: 0.7465 (ttt) REVERT: W 976 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7482 (mt-10) REVERT: W 1012 TYR cc_start: 0.8737 (m-80) cc_final: 0.8341 (m-80) REVERT: W 1014 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7601 (tmm) REVERT: W 1158 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: W 1277 MET cc_start: 0.8757 (mtt) cc_final: 0.8414 (mtp) REVERT: X 223 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7598 (mmm160) REVERT: X 301 GLU cc_start: 0.7803 (mp0) cc_final: 0.7431 (mp0) REVERT: X 366 GLU cc_start: 0.7372 (tp30) cc_final: 0.6846 (tp30) REVERT: X 499 MET cc_start: 0.7679 (mtp) cc_final: 0.7442 (mtp) REVERT: X 654 ASN cc_start: 0.6870 (m-40) cc_final: 0.6455 (t0) REVERT: X 676 ASP cc_start: 0.7757 (p0) cc_final: 0.7544 (p0) REVERT: X 835 ARG cc_start: 0.7537 (ttp-110) cc_final: 0.7206 (tmm-80) REVERT: Y 227 VAL cc_start: 0.9029 (t) cc_final: 0.8699 (m) REVERT: Z 482 ARG cc_start: 0.0707 (OUTLIER) cc_final: -0.0608 (tpp80) REVERT: 0 69 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7610 (tm-30) REVERT: 0 287 PHE cc_start: 0.8313 (m-80) cc_final: 0.7998 (m-80) REVERT: 0 303 GLU cc_start: 0.7859 (mp0) cc_final: 0.7582 (pm20) REVERT: 1 49 GLU cc_start: 0.8087 (tt0) cc_final: 0.7827 (tt0) REVERT: 1 86 ASP cc_start: 0.8686 (t0) cc_final: 0.8293 (m-30) REVERT: 1 103 SER cc_start: 0.8965 (t) cc_final: 0.8676 (m) REVERT: 1 144 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: 2 183 ASN cc_start: 0.7727 (m-40) cc_final: 0.6640 (t0) REVERT: 2 186 THR cc_start: 0.5137 (OUTLIER) cc_final: 0.4843 (p) REVERT: 3 173 MET cc_start: 0.9173 (mtm) cc_final: 0.8933 (mtm) REVERT: 4 80 GLN cc_start: 0.2910 (OUTLIER) cc_final: 0.1925 (tp40) outliers start: 245 outliers final: 147 residues processed: 879 average time/residue: 0.5500 time to fit residues: 833.0246 Evaluate side-chains 812 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 639 time to evaluate : 5.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 828 LEU Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain R residue 192 GLN Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 352 MET Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 580 SER Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 482 ARG Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 260 ASP Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 2 residue 186 THR Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 253 optimal weight: 0.4980 chunk 679 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 443 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 755 optimal weight: 10.0000 chunk 627 optimal weight: 0.9990 chunk 349 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 396 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN N 964 ASN O 697 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 ASN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 611 GLN Q 626 GLN R 30 HIS T 162 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN V 89 ASN W 455 HIS W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 63572 Z= 0.206 Angle : 0.582 11.036 86106 Z= 0.293 Chirality : 0.041 0.266 9878 Planarity : 0.004 0.058 10995 Dihedral : 4.835 89.120 8438 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 18.30 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 7758 helix: 2.16 (0.08), residues: 4273 sheet: -0.47 (0.17), residues: 844 loop : -1.85 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.023 0.001 PHE Y 195 TYR 0.021 0.001 TYR W 832 ARG 0.007 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 671 time to evaluate : 5.358 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: A 65 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4381 (mm) REVERT: A 77 MET cc_start: 0.1806 (mmp) cc_final: 0.1216 (ptt) REVERT: A 361 MET cc_start: 0.7513 (mmm) cc_final: 0.7015 (mtm) REVERT: D 66 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.3193 (mp) REVERT: D 108 GLN cc_start: 0.5235 (pt0) cc_final: 0.3476 (mm110) REVERT: D 182 MET cc_start: 0.1975 (OUTLIER) cc_final: 0.1468 (mmp) REVERT: F 174 ARG cc_start: 0.5225 (mmt180) cc_final: 0.4372 (ptt-90) REVERT: G 43 MET cc_start: -0.1566 (tmm) cc_final: -0.2408 (ptp) REVERT: G 44 MET cc_start: 0.1526 (ttp) cc_final: 0.0466 (mmt) REVERT: G 114 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.4824 (mt) REVERT: G 162 GLU cc_start: 0.3858 (pp20) cc_final: 0.2940 (tp30) REVERT: G 165 GLN cc_start: 0.4926 (OUTLIER) cc_final: 0.4584 (mp10) REVERT: H 158 GLU cc_start: 0.2570 (pp20) cc_final: 0.1120 (mm-30) REVERT: I 88 ASN cc_start: 0.3241 (OUTLIER) cc_final: 0.1412 (t0) REVERT: J 121 MET cc_start: -0.2596 (tpt) cc_final: -0.4336 (ptt) REVERT: K 57 GLN cc_start: 0.5384 (tp40) cc_final: 0.4680 (tt0) REVERT: K 77 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6805 (mm110) REVERT: K 92 MET cc_start: 0.7672 (mmt) cc_final: 0.7191 (mmt) REVERT: N 117 MET cc_start: -0.0031 (tmm) cc_final: -0.0447 (ptm) REVERT: N 299 PHE cc_start: 0.7640 (t80) cc_final: 0.7401 (t80) REVERT: N 305 LEU cc_start: 0.8398 (mt) cc_final: 0.8005 (tt) REVERT: N 375 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.5038 (p0) REVERT: N 547 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: N 674 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7212 (tm-30) REVERT: N 691 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8757 (tptp) REVERT: N 703 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7519 (ttp-110) REVERT: N 830 LYS cc_start: 0.7867 (mttt) cc_final: 0.7264 (mtmm) REVERT: O 714 ASP cc_start: 0.8031 (m-30) cc_final: 0.7446 (t0) REVERT: O 746 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7575 (m-40) REVERT: O 766 LYS cc_start: 0.8559 (mttt) cc_final: 0.8284 (mmtp) REVERT: P 51 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7788 (mp) REVERT: P 171 PHE cc_start: 0.8359 (t80) cc_final: 0.7940 (t80) REVERT: P 382 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8483 (mt) REVERT: P 472 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7584 (tmt170) REVERT: P 529 MET cc_start: 0.8415 (mtp) cc_final: 0.8159 (mtp) REVERT: P 598 ASN cc_start: 0.8316 (m110) cc_final: 0.7608 (t0) REVERT: P 745 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7985 (tppt) REVERT: P 754 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7808 (tpt170) REVERT: Q 264 GLN cc_start: 0.6239 (tm-30) cc_final: 0.5612 (mp10) REVERT: Q 478 LEU cc_start: 0.8452 (mp) cc_final: 0.8053 (tt) REVERT: Q 493 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8946 (mp) REVERT: R 32 LEU cc_start: 0.3354 (OUTLIER) cc_final: 0.3076 (tp) REVERT: R 119 MET cc_start: 0.7399 (mmm) cc_final: 0.7040 (ptt) REVERT: R 191 GLU cc_start: 0.7183 (pt0) cc_final: 0.6814 (mm-30) REVERT: R 201 LYS cc_start: 0.5951 (ttpt) cc_final: 0.4675 (pptt) REVERT: T 1 MET cc_start: 0.6366 (ptp) cc_final: 0.5800 (ptp) REVERT: T 81 ASN cc_start: 0.7760 (t0) cc_final: 0.7202 (t0) REVERT: T 153 CYS cc_start: 0.7909 (p) cc_final: 0.7661 (p) REVERT: T 204 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5890 (pp30) REVERT: U 61 LEU cc_start: 0.2365 (tp) cc_final: 0.1047 (pp) REVERT: V 78 LEU cc_start: 0.5168 (tt) cc_final: 0.4828 (mm) REVERT: W 4 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: W 37 LEU cc_start: 0.8490 (mt) cc_final: 0.8223 (mt) REVERT: W 230 VAL cc_start: 0.9541 (t) cc_final: 0.9302 (m) REVERT: W 310 TYR cc_start: 0.8454 (t80) cc_final: 0.8238 (t80) REVERT: W 343 LEU cc_start: 0.8588 (tt) cc_final: 0.8371 (mp) REVERT: W 373 MET cc_start: 0.8711 (mmm) cc_final: 0.8420 (mmm) REVERT: W 495 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6811 (pt) REVERT: W 739 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8535 (mp) REVERT: W 976 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7528 (mt-10) REVERT: W 1012 TYR cc_start: 0.8759 (m-80) cc_final: 0.8356 (m-80) REVERT: W 1014 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7595 (tmm) REVERT: W 1158 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: W 1277 MET cc_start: 0.8770 (mtt) cc_final: 0.8419 (mtp) REVERT: X 223 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7516 (mmm160) REVERT: X 301 GLU cc_start: 0.7830 (mp0) cc_final: 0.7469 (mp0) REVERT: X 341 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8807 (tt) REVERT: X 366 GLU cc_start: 0.7355 (tp30) cc_final: 0.6813 (tp30) REVERT: X 499 MET cc_start: 0.7625 (mtp) cc_final: 0.7260 (mtp) REVERT: X 654 ASN cc_start: 0.6855 (m-40) cc_final: 0.6421 (t0) REVERT: X 676 ASP cc_start: 0.7773 (p0) cc_final: 0.7549 (p0) REVERT: X 776 MET cc_start: 0.8533 (tpp) cc_final: 0.8264 (tpp) REVERT: X 893 MET cc_start: 0.8891 (mmm) cc_final: 0.8617 (tpp) REVERT: Y 145 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8475 (mt) REVERT: Y 227 VAL cc_start: 0.9024 (t) cc_final: 0.8700 (m) REVERT: 0 69 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7607 (tm-30) REVERT: 0 287 PHE cc_start: 0.8309 (m-80) cc_final: 0.8018 (m-80) REVERT: 1 86 ASP cc_start: 0.8641 (t0) cc_final: 0.8256 (m-30) REVERT: 1 103 SER cc_start: 0.8974 (t) cc_final: 0.8679 (m) REVERT: 1 144 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: 2 183 ASN cc_start: 0.7732 (m-40) cc_final: 0.6646 (t0) REVERT: 3 173 MET cc_start: 0.9173 (mtm) cc_final: 0.8909 (mtm) REVERT: 4 80 GLN cc_start: 0.3080 (OUTLIER) cc_final: 0.2026 (tp40) outliers start: 253 outliers final: 173 residues processed: 869 average time/residue: 0.5604 time to fit residues: 845.0367 Evaluate side-chains 841 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 642 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 691 LYS Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 621 LEU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 608 MET Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 129 GLN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 352 MET Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 341 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 580 SER Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 935 LEU Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 145 ILE Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 166 THR Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 258 MET Chi-restraints excluded: chain 0 residue 260 ASP Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 132 ASP Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 46 LYS Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 728 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 551 optimal weight: 3.9990 chunk 427 optimal weight: 0.7980 chunk 636 optimal weight: 0.5980 chunk 421 optimal weight: 1.9990 chunk 752 optimal weight: 0.9990 chunk 471 optimal weight: 0.9990 chunk 458 optimal weight: 0.8980 chunk 347 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 459 HIS O 697 HIS O 732 GLN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN W 345 GLN W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 63572 Z= 0.190 Angle : 0.573 10.856 86106 Z= 0.288 Chirality : 0.040 0.243 9878 Planarity : 0.004 0.070 10995 Dihedral : 4.715 89.031 8434 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 3.56 % Allowed : 18.90 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 7758 helix: 2.29 (0.08), residues: 4267 sheet: -0.42 (0.17), residues: 838 loop : -1.80 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.024 0.001 PHE Y 195 TYR 0.037 0.001 TYR P 840 ARG 0.006 0.000 ARG O 739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 688 time to evaluate : 5.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4724 (mm) REVERT: A 77 MET cc_start: 0.1362 (mmp) cc_final: 0.1089 (ptt) REVERT: A 361 MET cc_start: 0.7485 (mmm) cc_final: 0.7052 (mtm) REVERT: D 66 LEU cc_start: 0.3429 (OUTLIER) cc_final: 0.3185 (mp) REVERT: D 88 LYS cc_start: 0.5302 (mttt) cc_final: 0.4879 (mttm) REVERT: D 108 GLN cc_start: 0.5138 (pt0) cc_final: 0.3403 (mm-40) REVERT: D 182 MET cc_start: 0.2158 (OUTLIER) cc_final: 0.1752 (mmp) REVERT: F 174 ARG cc_start: 0.5347 (mmt180) cc_final: 0.4414 (ptt-90) REVERT: G 15 MET cc_start: 0.1123 (tpp) cc_final: 0.0915 (tpp) REVERT: G 43 MET cc_start: -0.1651 (tmm) cc_final: -0.2373 (ptp) REVERT: G 44 MET cc_start: 0.1524 (ttp) cc_final: 0.0546 (mmt) REVERT: G 114 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5126 (mt) REVERT: G 138 MET cc_start: 0.1577 (mtp) cc_final: 0.0132 (tpt) REVERT: G 162 GLU cc_start: 0.3670 (pp20) cc_final: 0.3063 (tp30) REVERT: G 165 GLN cc_start: 0.4991 (OUTLIER) cc_final: 0.3207 (pp30) REVERT: H 158 GLU cc_start: 0.2563 (pp20) cc_final: 0.1098 (mm-30) REVERT: I 88 ASN cc_start: 0.3256 (OUTLIER) cc_final: 0.1263 (t0) REVERT: I 104 MET cc_start: 0.4648 (tmm) cc_final: 0.3673 (tpt) REVERT: J 121 MET cc_start: -0.2606 (tpt) cc_final: -0.4237 (ptt) REVERT: K 77 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6834 (mm110) REVERT: K 92 MET cc_start: 0.7600 (mmt) cc_final: 0.7115 (mmt) REVERT: N 117 MET cc_start: -0.0013 (tmm) cc_final: -0.0440 (ptm) REVERT: N 299 PHE cc_start: 0.7655 (t80) cc_final: 0.7429 (t80) REVERT: N 305 LEU cc_start: 0.8424 (mt) cc_final: 0.8029 (tt) REVERT: N 375 ASP cc_start: 0.5290 (OUTLIER) cc_final: 0.5050 (p0) REVERT: N 547 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: N 674 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7274 (tm-30) REVERT: N 703 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7509 (ttp-110) REVERT: N 830 LYS cc_start: 0.7860 (mttt) cc_final: 0.7271 (mtmm) REVERT: O 714 ASP cc_start: 0.8057 (m-30) cc_final: 0.7468 (t0) REVERT: O 732 GLN cc_start: 0.4770 (OUTLIER) cc_final: 0.3450 (tp40) REVERT: O 746 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7594 (m-40) REVERT: O 766 LYS cc_start: 0.8516 (mttt) cc_final: 0.8204 (mmtp) REVERT: P 51 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (mt) REVERT: P 171 PHE cc_start: 0.8373 (t80) cc_final: 0.7966 (t80) REVERT: P 382 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8469 (mt) REVERT: P 472 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7645 (tmt170) REVERT: P 529 MET cc_start: 0.8403 (mtp) cc_final: 0.8103 (mtp) REVERT: P 598 ASN cc_start: 0.8271 (m110) cc_final: 0.7597 (t0) REVERT: P 745 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7951 (ttmt) REVERT: P 754 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7814 (tpt170) REVERT: Q 264 GLN cc_start: 0.6260 (tm-30) cc_final: 0.5633 (mp10) REVERT: Q 392 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.6149 (tpp) REVERT: Q 478 LEU cc_start: 0.8421 (mp) cc_final: 0.8060 (tt) REVERT: Q 493 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8915 (mp) REVERT: R 191 GLU cc_start: 0.7240 (pt0) cc_final: 0.6853 (mm-30) REVERT: R 201 LYS cc_start: 0.5844 (ttpt) cc_final: 0.4687 (pptt) REVERT: T 1 MET cc_start: 0.6407 (ptp) cc_final: 0.5850 (ptp) REVERT: T 63 MET cc_start: 0.5000 (ppp) cc_final: 0.4220 (ppp) REVERT: T 81 ASN cc_start: 0.7763 (t0) cc_final: 0.7194 (t0) REVERT: T 153 CYS cc_start: 0.7955 (p) cc_final: 0.7633 (p) REVERT: T 204 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6042 (pp30) REVERT: U 61 LEU cc_start: 0.2393 (tp) cc_final: 0.1051 (pp) REVERT: V 30 MET cc_start: 0.4400 (mmp) cc_final: 0.3241 (tmm) REVERT: V 78 LEU cc_start: 0.5208 (tt) cc_final: 0.4854 (mm) REVERT: W 37 LEU cc_start: 0.8498 (mt) cc_final: 0.8224 (mt) REVERT: W 230 VAL cc_start: 0.9539 (t) cc_final: 0.9295 (m) REVERT: W 310 TYR cc_start: 0.8451 (t80) cc_final: 0.8226 (t80) REVERT: W 343 LEU cc_start: 0.8638 (tt) cc_final: 0.8428 (mp) REVERT: W 373 MET cc_start: 0.8705 (mmm) cc_final: 0.8405 (mmm) REVERT: W 495 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6810 (pt) REVERT: W 739 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8535 (mp) REVERT: W 877 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7761 (t0) REVERT: W 976 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7483 (mt-10) REVERT: W 1012 TYR cc_start: 0.8737 (m-80) cc_final: 0.8333 (m-80) REVERT: W 1014 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7585 (tmm) REVERT: W 1158 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: W 1277 MET cc_start: 0.8756 (mtt) cc_final: 0.8406 (mtp) REVERT: X 223 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7550 (mmm160) REVERT: X 301 GLU cc_start: 0.7823 (mp0) cc_final: 0.7467 (mp0) REVERT: X 341 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8792 (tt) REVERT: X 366 GLU cc_start: 0.7358 (tp30) cc_final: 0.6822 (tp30) REVERT: X 499 MET cc_start: 0.7627 (mtp) cc_final: 0.7261 (mtp) REVERT: X 676 ASP cc_start: 0.7756 (p0) cc_final: 0.7536 (p0) REVERT: X 776 MET cc_start: 0.8538 (tpp) cc_final: 0.8255 (tpp) REVERT: X 893 MET cc_start: 0.8901 (mmm) cc_final: 0.8493 (tpp) REVERT: Y 135 ILE cc_start: 0.7431 (mp) cc_final: 0.6930 (mt) REVERT: Y 227 VAL cc_start: 0.9032 (t) cc_final: 0.8728 (m) REVERT: 0 69 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7477 (tm-30) REVERT: 0 237 GLN cc_start: 0.8067 (mp10) cc_final: 0.7830 (mp10) REVERT: 0 287 PHE cc_start: 0.8267 (m-80) cc_final: 0.8012 (m-80) REVERT: 1 86 ASP cc_start: 0.8638 (t0) cc_final: 0.8241 (m-30) REVERT: 1 103 SER cc_start: 0.8971 (t) cc_final: 0.8673 (m) REVERT: 1 144 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: 2 68 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7738 (mmmm) REVERT: 2 183 ASN cc_start: 0.7684 (m-40) cc_final: 0.6583 (t0) REVERT: 3 173 MET cc_start: 0.9161 (mtm) cc_final: 0.8939 (mtm) REVERT: 4 80 GLN cc_start: 0.2927 (OUTLIER) cc_final: 0.2047 (tp40) REVERT: 4 105 TRP cc_start: 0.1348 (OUTLIER) cc_final: 0.0897 (t60) outliers start: 244 outliers final: 180 residues processed: 878 average time/residue: 0.5538 time to fit residues: 842.6192 Evaluate side-chains 853 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 647 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 292 MET Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain O residue 732 GLN Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 198 GLN Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 490 ASP Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 648 ASP Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 392 MET Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 517 GLN Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 352 MET Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 877 ASN Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 341 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 580 SER Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 258 MET Chi-restraints excluded: chain 0 residue 260 ASP Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 80 ASP Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 465 optimal weight: 0.3980 chunk 300 optimal weight: 1.9990 chunk 449 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 145 optimal weight: 220.0000 chunk 478 optimal weight: 0.5980 chunk 512 optimal weight: 4.9990 chunk 372 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 591 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 697 HIS O 705 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 HIS Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 GLN U 129 GLN W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 428 HIS ** Z 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 ASN 3 162 GLN ** 4 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63572 Z= 0.181 Angle : 0.571 12.502 86106 Z= 0.286 Chirality : 0.040 0.303 9878 Planarity : 0.004 0.062 10995 Dihedral : 4.608 89.679 8432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 3.43 % Allowed : 19.28 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 7758 helix: 2.37 (0.08), residues: 4270 sheet: -0.34 (0.18), residues: 830 loop : -1.77 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.025 0.001 PHE Y 195 TYR 0.028 0.001 TYR 4 51 ARG 0.008 0.000 ARG P 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 667 time to evaluate : 5.522 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: A 65 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4731 (mm) REVERT: A 77 MET cc_start: 0.1518 (mmp) cc_final: 0.1188 (ptt) REVERT: A 361 MET cc_start: 0.7461 (mmm) cc_final: 0.7099 (mtm) REVERT: A 378 LYS cc_start: 0.6288 (pttp) cc_final: 0.5835 (ttmt) REVERT: D 66 LEU cc_start: 0.3347 (OUTLIER) cc_final: 0.3130 (mp) REVERT: D 88 LYS cc_start: 0.5289 (mttt) cc_final: 0.4874 (mttm) REVERT: D 108 GLN cc_start: 0.5103 (pt0) cc_final: 0.3420 (mm-40) REVERT: D 180 LEU cc_start: 0.3687 (OUTLIER) cc_final: 0.3435 (pp) REVERT: D 182 MET cc_start: 0.2451 (OUTLIER) cc_final: 0.2193 (mmp) REVERT: F 174 ARG cc_start: 0.5335 (mmt180) cc_final: 0.4383 (ptt-90) REVERT: G 43 MET cc_start: -0.1637 (tmm) cc_final: -0.2331 (ptp) REVERT: G 44 MET cc_start: 0.1941 (ttp) cc_final: 0.1006 (mmt) REVERT: G 114 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5110 (mt) REVERT: G 138 MET cc_start: 0.1363 (mtp) cc_final: -0.0123 (tpt) REVERT: G 162 GLU cc_start: 0.3632 (pp20) cc_final: 0.3051 (tp30) REVERT: G 165 GLN cc_start: 0.4940 (OUTLIER) cc_final: 0.3266 (pp30) REVERT: H 158 GLU cc_start: 0.2563 (pp20) cc_final: 0.1091 (mm-30) REVERT: I 88 ASN cc_start: 0.3239 (OUTLIER) cc_final: 0.1198 (t0) REVERT: I 104 MET cc_start: 0.4748 (tmm) cc_final: 0.3785 (tpt) REVERT: J 121 MET cc_start: -0.2588 (tpt) cc_final: -0.4290 (ptt) REVERT: K 77 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6843 (mm110) REVERT: K 116 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6350 (tp30) REVERT: N 117 MET cc_start: 0.0046 (tmm) cc_final: -0.0384 (ptm) REVERT: N 299 PHE cc_start: 0.7677 (t80) cc_final: 0.7442 (t80) REVERT: N 305 LEU cc_start: 0.8371 (mt) cc_final: 0.8058 (tt) REVERT: N 375 ASP cc_start: 0.5411 (OUTLIER) cc_final: 0.5122 (p0) REVERT: N 547 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: N 674 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7285 (tm-30) REVERT: N 830 LYS cc_start: 0.7859 (mttt) cc_final: 0.7287 (mtmm) REVERT: O 714 ASP cc_start: 0.8104 (m-30) cc_final: 0.7511 (t0) REVERT: O 746 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7601 (m-40) REVERT: O 766 LYS cc_start: 0.8527 (mttt) cc_final: 0.8248 (mmtp) REVERT: P 171 PHE cc_start: 0.8355 (t80) cc_final: 0.7922 (t80) REVERT: P 382 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8469 (mt) REVERT: P 472 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7642 (tmt170) REVERT: P 529 MET cc_start: 0.8422 (mtp) cc_final: 0.8115 (mtp) REVERT: P 598 ASN cc_start: 0.8268 (m110) cc_final: 0.7644 (t0) REVERT: P 745 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7939 (ttmt) REVERT: P 754 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7791 (tpt170) REVERT: Q 217 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8392 (Cg_endo) REVERT: Q 264 GLN cc_start: 0.6263 (tm-30) cc_final: 0.5650 (mp10) REVERT: Q 392 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6173 (tpp) REVERT: Q 478 LEU cc_start: 0.8403 (mp) cc_final: 0.8069 (tt) REVERT: R 191 GLU cc_start: 0.7247 (pt0) cc_final: 0.6884 (mm-30) REVERT: R 201 LYS cc_start: 0.5815 (ttpt) cc_final: 0.4683 (pptt) REVERT: T 1 MET cc_start: 0.6374 (ptp) cc_final: 0.5761 (ptp) REVERT: T 46 TYR cc_start: 0.7409 (m-10) cc_final: 0.7209 (m-10) REVERT: T 63 MET cc_start: 0.4982 (ppp) cc_final: 0.4145 (ppp) REVERT: T 81 ASN cc_start: 0.7738 (t0) cc_final: 0.7240 (t0) REVERT: T 153 CYS cc_start: 0.7948 (p) cc_final: 0.7639 (p) REVERT: T 194 MET cc_start: 0.7382 (tmm) cc_final: 0.7042 (ttp) REVERT: T 204 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5903 (pp30) REVERT: U 61 LEU cc_start: 0.2132 (tp) cc_final: 0.0827 (pp) REVERT: V 30 MET cc_start: 0.4275 (mmp) cc_final: 0.3144 (tmm) REVERT: V 78 LEU cc_start: 0.5166 (tt) cc_final: 0.4810 (mm) REVERT: W 37 LEU cc_start: 0.8523 (mt) cc_final: 0.8243 (mt) REVERT: W 230 VAL cc_start: 0.9535 (t) cc_final: 0.9287 (m) REVERT: W 310 TYR cc_start: 0.8443 (t80) cc_final: 0.8219 (t80) REVERT: W 343 LEU cc_start: 0.8639 (tt) cc_final: 0.8425 (mp) REVERT: W 373 MET cc_start: 0.8705 (mmm) cc_final: 0.8319 (mmm) REVERT: W 495 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6766 (pt) REVERT: W 739 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (mp) REVERT: W 877 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7758 (t0) REVERT: W 976 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7406 (mt-10) REVERT: W 1012 TYR cc_start: 0.8729 (m-80) cc_final: 0.8274 (m-80) REVERT: W 1014 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7564 (tmm) REVERT: W 1158 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: W 1277 MET cc_start: 0.8755 (mtt) cc_final: 0.8407 (mtp) REVERT: X 223 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7554 (mmm160) REVERT: X 301 GLU cc_start: 0.7820 (mp0) cc_final: 0.7477 (mp0) REVERT: X 341 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8799 (tt) REVERT: X 366 GLU cc_start: 0.7396 (tp30) cc_final: 0.6821 (tp30) REVERT: X 499 MET cc_start: 0.7617 (mtp) cc_final: 0.7262 (mtp) REVERT: X 676 ASP cc_start: 0.7750 (p0) cc_final: 0.7533 (p0) REVERT: X 776 MET cc_start: 0.8559 (tpp) cc_final: 0.8272 (tpp) REVERT: X 893 MET cc_start: 0.8913 (mmm) cc_final: 0.8492 (tpp) REVERT: Y 135 ILE cc_start: 0.7491 (mp) cc_final: 0.6986 (mt) REVERT: Y 227 VAL cc_start: 0.9042 (t) cc_final: 0.8737 (m) REVERT: 0 43 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6453 (mt-10) REVERT: 0 69 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7532 (tm-30) REVERT: 0 237 GLN cc_start: 0.8068 (mp10) cc_final: 0.7784 (mp10) REVERT: 0 287 PHE cc_start: 0.8258 (m-80) cc_final: 0.8039 (m-80) REVERT: 1 86 ASP cc_start: 0.8639 (t0) cc_final: 0.8236 (m-30) REVERT: 1 103 SER cc_start: 0.8965 (t) cc_final: 0.8662 (m) REVERT: 1 144 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: 2 126 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7574 (m) REVERT: 2 183 ASN cc_start: 0.7647 (m-40) cc_final: 0.6565 (t0) REVERT: 3 173 MET cc_start: 0.9160 (mtm) cc_final: 0.8927 (mtm) REVERT: 4 23 GLU cc_start: 0.2633 (mm-30) cc_final: 0.0600 (tt0) REVERT: 4 80 GLN cc_start: 0.3070 (OUTLIER) cc_final: 0.2257 (tp40) REVERT: 4 105 TRP cc_start: 0.1355 (OUTLIER) cc_final: 0.0916 (t60) outliers start: 235 outliers final: 178 residues processed: 847 average time/residue: 0.5589 time to fit residues: 821.2753 Evaluate side-chains 849 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 646 time to evaluate : 5.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 802 VAL Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 820 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 950 VAL Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 382 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 490 ASP Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 648 ASP Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 159 ILE Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 261 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 392 MET Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 352 MET Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 600 ILE Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 877 ASN Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 341 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 580 SER Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 935 LEU Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 166 THR Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 258 MET Chi-restraints excluded: chain 0 residue 274 ILE Chi-restraints excluded: chain 1 residue 141 GLN Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 99 ILE Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 3 residue 80 ASP Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 684 optimal weight: 0.7980 chunk 721 optimal weight: 3.9990 chunk 657 optimal weight: 1.9990 chunk 701 optimal weight: 0.0030 chunk 720 optimal weight: 0.6980 chunk 422 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 550 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 633 optimal weight: 0.9990 chunk 663 optimal weight: 0.0980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 HIS Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 564 ASN ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63572 Z= 0.168 Angle : 0.571 11.686 86106 Z= 0.284 Chirality : 0.040 0.273 9878 Planarity : 0.004 0.064 10995 Dihedral : 4.529 89.433 8432 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 3.09 % Allowed : 19.73 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 7758 helix: 2.44 (0.08), residues: 4270 sheet: -0.29 (0.18), residues: 825 loop : -1.73 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.027 0.001 PHE W 789 TYR 0.018 0.001 TYR R 167 ARG 0.008 0.000 ARG P 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 678 time to evaluate : 5.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.4930 (OUTLIER) cc_final: 0.4723 (mm) REVERT: A 77 MET cc_start: 0.1651 (mmp) cc_final: 0.1292 (ptt) REVERT: D 66 LEU cc_start: 0.3366 (OUTLIER) cc_final: 0.3139 (mp) REVERT: D 85 ASN cc_start: 0.4862 (m-40) cc_final: 0.4578 (m-40) REVERT: D 88 LYS cc_start: 0.5265 (mttt) cc_final: 0.4923 (tttm) REVERT: D 108 GLN cc_start: 0.5085 (pt0) cc_final: 0.3445 (mm-40) REVERT: D 180 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3591 (pp) REVERT: G 43 MET cc_start: -0.1517 (tmm) cc_final: -0.2549 (ptp) REVERT: G 44 MET cc_start: 0.1819 (ttp) cc_final: 0.1060 (mmt) REVERT: G 114 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5043 (mt) REVERT: G 138 MET cc_start: 0.1109 (mtp) cc_final: -0.0141 (tpt) REVERT: G 165 GLN cc_start: 0.4955 (OUTLIER) cc_final: 0.3813 (pp30) REVERT: H 158 GLU cc_start: 0.2560 (pp20) cc_final: 0.1064 (mm-30) REVERT: I 88 ASN cc_start: 0.3162 (OUTLIER) cc_final: 0.1128 (t0) REVERT: I 104 MET cc_start: 0.4709 (tmm) cc_final: 0.3761 (tpt) REVERT: J 121 MET cc_start: -0.2571 (tpt) cc_final: -0.4286 (ptt) REVERT: K 77 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6802 (mm110) REVERT: K 92 MET cc_start: 0.7571 (mmt) cc_final: 0.7061 (mmt) REVERT: K 116 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6349 (tp30) REVERT: N 117 MET cc_start: 0.0045 (tmm) cc_final: -0.0387 (ptm) REVERT: N 305 LEU cc_start: 0.8386 (mt) cc_final: 0.8045 (tt) REVERT: N 375 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.5094 (p0) REVERT: N 547 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: N 674 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7293 (tm-30) REVERT: N 830 LYS cc_start: 0.7881 (mttt) cc_final: 0.7305 (mtmm) REVERT: O 714 ASP cc_start: 0.8083 (m-30) cc_final: 0.7453 (t0) REVERT: O 766 LYS cc_start: 0.8520 (mttt) cc_final: 0.8243 (mmtp) REVERT: P 472 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7646 (tmt170) REVERT: P 529 MET cc_start: 0.8408 (mtp) cc_final: 0.8104 (mtp) REVERT: P 598 ASN cc_start: 0.8207 (m110) cc_final: 0.7793 (t0) REVERT: P 754 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7763 (tpt170) REVERT: P 825 LYS cc_start: 0.8748 (ptmt) cc_final: 0.8517 (tptt) REVERT: Q 264 GLN cc_start: 0.6149 (tm-30) cc_final: 0.5595 (mp10) REVERT: Q 392 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5952 (tpp) REVERT: Q 415 LYS cc_start: 0.7952 (mttt) cc_final: 0.7314 (tptp) REVERT: Q 478 LEU cc_start: 0.8398 (mp) cc_final: 0.8075 (tt) REVERT: R 191 GLU cc_start: 0.7180 (pt0) cc_final: 0.6396 (mt-10) REVERT: R 201 LYS cc_start: 0.5821 (ttpt) cc_final: 0.4640 (pptt) REVERT: T 1 MET cc_start: 0.6398 (ptp) cc_final: 0.5769 (ptp) REVERT: T 46 TYR cc_start: 0.7285 (m-10) cc_final: 0.7084 (m-10) REVERT: T 63 MET cc_start: 0.4641 (ppp) cc_final: 0.3930 (ppp) REVERT: T 81 ASN cc_start: 0.7868 (t0) cc_final: 0.7391 (t0) REVERT: T 153 CYS cc_start: 0.7940 (p) cc_final: 0.7626 (p) REVERT: T 204 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5946 (pp30) REVERT: U 61 LEU cc_start: 0.2164 (tp) cc_final: 0.0866 (pp) REVERT: V 30 MET cc_start: 0.4132 (mmp) cc_final: 0.3182 (tmm) REVERT: V 78 LEU cc_start: 0.4972 (tt) cc_final: 0.4754 (mm) REVERT: W 25 MET cc_start: 0.6609 (tpp) cc_final: 0.6274 (mmp) REVERT: W 37 LEU cc_start: 0.8519 (mt) cc_final: 0.8236 (mt) REVERT: W 230 VAL cc_start: 0.9529 (t) cc_final: 0.9278 (m) REVERT: W 306 ASP cc_start: 0.8445 (t0) cc_final: 0.8023 (m-30) REVERT: W 338 LEU cc_start: 0.9333 (mt) cc_final: 0.9123 (mm) REVERT: W 343 LEU cc_start: 0.8585 (tt) cc_final: 0.8365 (mp) REVERT: W 373 MET cc_start: 0.8695 (mmm) cc_final: 0.8320 (mmm) REVERT: W 495 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6751 (pt) REVERT: W 660 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: W 739 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8463 (mp) REVERT: W 877 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7776 (t0) REVERT: W 976 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7372 (mt-10) REVERT: W 1012 TYR cc_start: 0.8745 (m-80) cc_final: 0.8290 (m-80) REVERT: W 1014 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7589 (tmm) REVERT: W 1158 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: W 1180 GLU cc_start: 0.7778 (tp30) cc_final: 0.7477 (tp30) REVERT: W 1277 MET cc_start: 0.8741 (mtt) cc_final: 0.8388 (mtp) REVERT: X 223 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7572 (mmm160) REVERT: X 301 GLU cc_start: 0.7810 (mp0) cc_final: 0.7466 (mp0) REVERT: X 341 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8770 (tt) REVERT: X 366 GLU cc_start: 0.7380 (tp30) cc_final: 0.6809 (tp30) REVERT: X 420 ILE cc_start: 0.7531 (mm) cc_final: 0.7291 (mt) REVERT: X 499 MET cc_start: 0.7602 (mtp) cc_final: 0.7274 (mtp) REVERT: X 676 ASP cc_start: 0.7717 (p0) cc_final: 0.7494 (p0) REVERT: X 776 MET cc_start: 0.8566 (tpp) cc_final: 0.8286 (tpp) REVERT: X 893 MET cc_start: 0.8882 (mmm) cc_final: 0.8485 (tpp) REVERT: Y 135 ILE cc_start: 0.7511 (mp) cc_final: 0.6996 (mt) REVERT: Y 227 VAL cc_start: 0.9033 (t) cc_final: 0.8726 (m) REVERT: 0 69 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7581 (tm-30) REVERT: 0 237 GLN cc_start: 0.8054 (mp10) cc_final: 0.7766 (mp10) REVERT: 0 287 PHE cc_start: 0.8200 (m-80) cc_final: 0.7994 (m-80) REVERT: 1 103 SER cc_start: 0.8936 (t) cc_final: 0.8641 (m) REVERT: 1 144 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: 2 126 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7570 (m) REVERT: 2 183 ASN cc_start: 0.7646 (m-40) cc_final: 0.6583 (t0) REVERT: 3 173 MET cc_start: 0.9143 (mtm) cc_final: 0.8908 (mtm) REVERT: 4 23 GLU cc_start: 0.2626 (mm-30) cc_final: 0.0602 (tt0) REVERT: 4 80 GLN cc_start: 0.3113 (OUTLIER) cc_final: 0.2261 (tp40) REVERT: 4 105 TRP cc_start: 0.1341 (OUTLIER) cc_final: 0.0928 (t60) outliers start: 212 outliers final: 160 residues processed: 842 average time/residue: 0.5699 time to fit residues: 834.0070 Evaluate side-chains 824 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 641 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 804 ASN Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 858 MET Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 490 ASP Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 392 MET Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 517 GLN Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 89 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 458 LEU Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 600 ILE Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 877 ASN Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 341 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 569 LEU Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 935 LEU Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 258 MET Chi-restraints excluded: chain 1 residue 141 GLN Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 99 ILE Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 3 residue 80 ASP Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 699 optimal weight: 0.9980 chunk 460 optimal weight: 0.9990 chunk 741 optimal weight: 0.7980 chunk 452 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 chunk 515 optimal weight: 0.6980 chunk 778 optimal weight: 0.1980 chunk 716 optimal weight: 0.9980 chunk 619 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 478 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN N 201 HIS ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 HIS Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 GLN ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63572 Z= 0.181 Angle : 0.579 12.649 86106 Z= 0.287 Chirality : 0.040 0.234 9878 Planarity : 0.004 0.072 10995 Dihedral : 4.512 89.017 8431 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.95 % Allowed : 20.07 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 7758 helix: 2.45 (0.08), residues: 4271 sheet: -0.28 (0.18), residues: 829 loop : -1.71 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.026 0.001 PHE Y 195 TYR 0.020 0.001 TYR R 167 ARG 0.008 0.000 ARG P 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15516 Ramachandran restraints generated. 7758 Oldfield, 0 Emsley, 7758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 661 time to evaluate : 7.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4576 (mm) REVERT: D 66 LEU cc_start: 0.3395 (OUTLIER) cc_final: 0.3190 (mp) REVERT: D 85 ASN cc_start: 0.4866 (m-40) cc_final: 0.4569 (m-40) REVERT: D 88 LYS cc_start: 0.5372 (mttt) cc_final: 0.5031 (tttm) REVERT: D 108 GLN cc_start: 0.5098 (pt0) cc_final: 0.3458 (mm-40) REVERT: D 180 LEU cc_start: 0.3706 (OUTLIER) cc_final: 0.3460 (pp) REVERT: G 43 MET cc_start: -0.1492 (tmm) cc_final: -0.2442 (ptp) REVERT: G 44 MET cc_start: 0.1750 (ttp) cc_final: 0.1004 (mmp) REVERT: G 114 LEU cc_start: 0.5415 (OUTLIER) cc_final: 0.4960 (mt) REVERT: G 138 MET cc_start: 0.0991 (mtp) cc_final: -0.0242 (tpt) REVERT: G 165 GLN cc_start: 0.4988 (OUTLIER) cc_final: 0.3821 (pp30) REVERT: H 158 GLU cc_start: 0.2570 (pp20) cc_final: 0.1063 (mm-30) REVERT: I 88 ASN cc_start: 0.3234 (OUTLIER) cc_final: 0.1268 (t0) REVERT: I 104 MET cc_start: 0.4718 (tmm) cc_final: 0.3850 (tpt) REVERT: J 121 MET cc_start: -0.2535 (tpt) cc_final: -0.4274 (ptt) REVERT: K 77 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6962 (mm110) REVERT: K 92 MET cc_start: 0.7601 (mmt) cc_final: 0.7139 (mmt) REVERT: K 116 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6347 (tp30) REVERT: N 117 MET cc_start: 0.0058 (tmm) cc_final: -0.0384 (ptm) REVERT: N 305 LEU cc_start: 0.8367 (mt) cc_final: 0.8020 (tt) REVERT: N 375 ASP cc_start: 0.5265 (OUTLIER) cc_final: 0.5040 (p0) REVERT: N 450 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7193 (mt-10) REVERT: N 547 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: N 674 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7521 (tm-30) REVERT: N 830 LYS cc_start: 0.7845 (mttt) cc_final: 0.7297 (mtmm) REVERT: O 714 ASP cc_start: 0.8155 (m-30) cc_final: 0.7508 (t0) REVERT: O 766 LYS cc_start: 0.8498 (mttt) cc_final: 0.8236 (mmtp) REVERT: P 472 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7572 (tmt170) REVERT: P 529 MET cc_start: 0.8412 (mtp) cc_final: 0.8106 (mtp) REVERT: P 598 ASN cc_start: 0.8307 (m110) cc_final: 0.7692 (t0) REVERT: P 754 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7771 (tpt170) REVERT: Q 264 GLN cc_start: 0.6230 (tm-30) cc_final: 0.5582 (mp10) REVERT: Q 415 LYS cc_start: 0.7892 (mttt) cc_final: 0.7281 (tptp) REVERT: Q 478 LEU cc_start: 0.8420 (mp) cc_final: 0.8075 (tt) REVERT: Q 493 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8912 (mp) REVERT: R 191 GLU cc_start: 0.7125 (pt0) cc_final: 0.6830 (mm-30) REVERT: R 201 LYS cc_start: 0.5967 (ttpt) cc_final: 0.4725 (pptt) REVERT: T 1 MET cc_start: 0.6531 (ptp) cc_final: 0.5857 (ptp) REVERT: T 63 MET cc_start: 0.4685 (ppp) cc_final: 0.3960 (ppp) REVERT: T 81 ASN cc_start: 0.7857 (t0) cc_final: 0.7388 (t0) REVERT: T 153 CYS cc_start: 0.7955 (p) cc_final: 0.7622 (p) REVERT: T 204 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5965 (pp30) REVERT: U 61 LEU cc_start: 0.2160 (tp) cc_final: 0.0827 (pp) REVERT: V 30 MET cc_start: 0.4056 (mmp) cc_final: 0.3171 (tmm) REVERT: V 78 LEU cc_start: 0.5004 (tt) cc_final: 0.4782 (mm) REVERT: W 25 MET cc_start: 0.6523 (tpp) cc_final: 0.6211 (mmp) REVERT: W 37 LEU cc_start: 0.8526 (mt) cc_final: 0.8253 (mt) REVERT: W 230 VAL cc_start: 0.9523 (t) cc_final: 0.9265 (m) REVERT: W 306 ASP cc_start: 0.8439 (t0) cc_final: 0.8026 (m-30) REVERT: W 338 LEU cc_start: 0.9317 (mt) cc_final: 0.9104 (mm) REVERT: W 343 LEU cc_start: 0.8571 (tt) cc_final: 0.8356 (mp) REVERT: W 373 MET cc_start: 0.8701 (mmm) cc_final: 0.8326 (mmm) REVERT: W 495 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6755 (pt) REVERT: W 660 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: W 739 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8469 (mp) REVERT: W 877 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7789 (t0) REVERT: W 976 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7409 (mt-10) REVERT: W 1012 TYR cc_start: 0.8732 (m-80) cc_final: 0.8282 (m-80) REVERT: W 1014 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7564 (tmm) REVERT: W 1158 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: W 1180 GLU cc_start: 0.7741 (tp30) cc_final: 0.7455 (tp30) REVERT: W 1277 MET cc_start: 0.8743 (mtt) cc_final: 0.8388 (mtp) REVERT: X 223 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7606 (mmm160) REVERT: X 301 GLU cc_start: 0.7811 (mp0) cc_final: 0.7468 (mp0) REVERT: X 341 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8786 (tt) REVERT: X 366 GLU cc_start: 0.7392 (tp30) cc_final: 0.6821 (tp30) REVERT: X 420 ILE cc_start: 0.7521 (mm) cc_final: 0.7270 (mt) REVERT: X 499 MET cc_start: 0.7609 (mtp) cc_final: 0.7289 (mtp) REVERT: X 676 ASP cc_start: 0.7763 (p0) cc_final: 0.7554 (p0) REVERT: X 893 MET cc_start: 0.8880 (mmm) cc_final: 0.8479 (tpp) REVERT: Y 135 ILE cc_start: 0.7524 (mp) cc_final: 0.7009 (mt) REVERT: Y 227 VAL cc_start: 0.9041 (t) cc_final: 0.8744 (m) REVERT: 0 69 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7603 (tm-30) REVERT: 0 204 MET cc_start: 0.8332 (mtp) cc_final: 0.8118 (mtp) REVERT: 0 237 GLN cc_start: 0.8070 (mp10) cc_final: 0.7746 (mp10) REVERT: 1 86 ASP cc_start: 0.8661 (t0) cc_final: 0.8320 (t0) REVERT: 1 103 SER cc_start: 0.8936 (t) cc_final: 0.8631 (m) REVERT: 1 144 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: 2 126 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7611 (m) REVERT: 2 183 ASN cc_start: 0.7684 (m-40) cc_final: 0.6600 (t0) REVERT: 3 173 MET cc_start: 0.9141 (mtm) cc_final: 0.8875 (mtm) REVERT: 4 23 GLU cc_start: 0.2542 (mm-30) cc_final: 0.0197 (tt0) REVERT: 4 80 GLN cc_start: 0.3105 (OUTLIER) cc_final: 0.2271 (tp40) REVERT: 4 105 TRP cc_start: 0.1334 (OUTLIER) cc_final: 0.0935 (t60) outliers start: 202 outliers final: 163 residues processed: 824 average time/residue: 0.5581 time to fit residues: 800.3279 Evaluate side-chains 828 residues out of total 7070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 642 time to evaluate : 5.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 165 GLN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 372 ILE Chi-restraints excluded: chain N residue 375 ASP Chi-restraints excluded: chain N residue 424 ASN Chi-restraints excluded: chain N residue 440 VAL Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 471 ASP Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 525 TYR Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 547 GLN Chi-restraints excluded: chain N residue 557 VAL Chi-restraints excluded: chain N residue 573 VAL Chi-restraints excluded: chain N residue 690 CYS Chi-restraints excluded: chain N residue 709 THR Chi-restraints excluded: chain N residue 748 THR Chi-restraints excluded: chain N residue 757 VAL Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 837 THR Chi-restraints excluded: chain N residue 844 CYS Chi-restraints excluded: chain N residue 951 GLU Chi-restraints excluded: chain N residue 965 MET Chi-restraints excluded: chain O residue 708 CYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 124 SER Chi-restraints excluded: chain P residue 167 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 397 LEU Chi-restraints excluded: chain P residue 401 THR Chi-restraints excluded: chain P residue 556 ILE Chi-restraints excluded: chain P residue 564 LEU Chi-restraints excluded: chain P residue 682 THR Chi-restraints excluded: chain P residue 710 ASP Chi-restraints excluded: chain P residue 716 GLU Chi-restraints excluded: chain P residue 730 ASP Chi-restraints excluded: chain P residue 743 GLN Chi-restraints excluded: chain P residue 754 ARG Chi-restraints excluded: chain P residue 803 CYS Chi-restraints excluded: chain Q residue 21 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 421 LEU Chi-restraints excluded: chain Q residue 428 LEU Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 493 LEU Chi-restraints excluded: chain Q residue 517 GLN Chi-restraints excluded: chain Q residue 530 SER Chi-restraints excluded: chain Q residue 543 VAL Chi-restraints excluded: chain Q residue 592 ILE Chi-restraints excluded: chain Q residue 593 MET Chi-restraints excluded: chain Q residue 622 PHE Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 164 PHE Chi-restraints excluded: chain T residue 204 GLN Chi-restraints excluded: chain U residue 129 GLN Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 29 THR Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 281 ASP Chi-restraints excluded: chain W residue 370 ASP Chi-restraints excluded: chain W residue 389 LEU Chi-restraints excluded: chain W residue 419 SER Chi-restraints excluded: chain W residue 495 LEU Chi-restraints excluded: chain W residue 498 THR Chi-restraints excluded: chain W residue 572 VAL Chi-restraints excluded: chain W residue 600 ILE Chi-restraints excluded: chain W residue 660 GLU Chi-restraints excluded: chain W residue 691 LEU Chi-restraints excluded: chain W residue 714 ASP Chi-restraints excluded: chain W residue 739 LEU Chi-restraints excluded: chain W residue 797 LEU Chi-restraints excluded: chain W residue 806 ILE Chi-restraints excluded: chain W residue 861 THR Chi-restraints excluded: chain W residue 862 LEU Chi-restraints excluded: chain W residue 863 ASP Chi-restraints excluded: chain W residue 867 LEU Chi-restraints excluded: chain W residue 877 ASN Chi-restraints excluded: chain W residue 908 SER Chi-restraints excluded: chain W residue 999 ASP Chi-restraints excluded: chain W residue 1014 MET Chi-restraints excluded: chain W residue 1036 ASP Chi-restraints excluded: chain W residue 1158 GLU Chi-restraints excluded: chain W residue 1172 ILE Chi-restraints excluded: chain W residue 1241 THR Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 109 SER Chi-restraints excluded: chain X residue 180 ILE Chi-restraints excluded: chain X residue 189 TRP Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 274 GLN Chi-restraints excluded: chain X residue 280 LEU Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 341 LEU Chi-restraints excluded: chain X residue 417 VAL Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain X residue 554 VAL Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 VAL Chi-restraints excluded: chain X residue 819 SER Chi-restraints excluded: chain X residue 830 THR Chi-restraints excluded: chain X residue 935 LEU Chi-restraints excluded: chain X residue 952 VAL Chi-restraints excluded: chain X residue 968 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 148 SER Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 490 LEU Chi-restraints excluded: chain 0 residue 77 VAL Chi-restraints excluded: chain 0 residue 258 MET Chi-restraints excluded: chain 0 residue 260 ASP Chi-restraints excluded: chain 1 residue 141 GLN Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 2 residue 96 ASP Chi-restraints excluded: chain 2 residue 99 ILE Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 126 CYS Chi-restraints excluded: chain 2 residue 133 SER Chi-restraints excluded: chain 3 residue 80 ASP Chi-restraints excluded: chain 3 residue 142 ILE Chi-restraints excluded: chain 4 residue 80 GLN Chi-restraints excluded: chain 4 residue 105 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 781 random chunks: chunk 379 optimal weight: 0.9990 chunk 492 optimal weight: 0.8980 chunk 660 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 571 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 620 optimal weight: 0.3980 chunk 259 optimal weight: 0.9980 chunk 637 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN N 294 ASN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 HIS Q 517 GLN ** Q 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1198 GLN ** X 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120411 restraints weight = 129380.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114858 restraints weight = 92030.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115075 restraints weight = 82583.706| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63572 Z= 0.210 Angle : 0.595 11.941 86106 Z= 0.295 Chirality : 0.041 0.277 9878 Planarity : 0.004 0.072 10995 Dihedral : 4.536 88.775 8431 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 2.98 % Allowed : 20.20 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 7758 helix: 2.43 (0.08), residues: 4270 sheet: -0.26 (0.18), residues: 819 loop : -1.70 (0.12), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 105 HIS 0.009 0.001 HIS K 58 PHE 0.031 0.001 PHE 0 287 TYR 0.021 0.001 TYR R 167 ARG 0.008 0.000 ARG P 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14906.18 seconds wall clock time: 262 minutes 50.05 seconds (15770.05 seconds total)