Starting phenix.real_space_refine on Thu Mar 21 10:09:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ee8_9039/03_2024/6ee8_9039_neut.pdb" } resolution = 3.92 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= 0.007 sd= 0.065 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18270 2.51 5 N 5323 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 760": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 866": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29784 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1228 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 109.432 60.877 82.960 1.00169.12 S ATOM 19692 SG CYS D 968 106.034 61.770 84.984 1.00174.51 S ATOM 19734 SG CYS D 975 106.982 63.228 81.798 1.00161.34 S ATOM 19752 SG CYS D 978 106.509 59.787 80.902 1.00164.55 S ATOM 12567 SG CYS D 60 80.575 107.049 123.762 1.00178.81 S ATOM 12585 SG CYS D 62 79.844 107.368 127.301 1.00173.66 S ATOM 12720 SG CYS D 78 82.010 104.201 126.479 1.00175.82 S Time building chain proxies: 17.18, per 1000 atoms: 0.58 Number of scatterers: 29784 At special positions: 0 Unit cell: (135.2, 180.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 125 15.00 Mg 1 11.99 O 5964 8.00 N 5323 7.00 C 18270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.05 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 44 sheets defined 42.7% alpha, 15.1% beta 56 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 11.07 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.785A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.910A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.540A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.443A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.570A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.720A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.954A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.511A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.644A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.558A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 removed outlier: 3.540A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.627A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.285A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.600A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.388A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 5.485A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.700A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.727A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.299A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.080A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.321A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 removed outlier: 3.584A pdb=" N GLY D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.553A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.044A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 removed outlier: 4.100A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.592A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.859A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.517A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.579A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.921A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.102A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.757A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.667A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.529A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.661A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 4.184A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.595A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.249A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.185A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.626A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.820A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.885A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.742A pdb=" N GLU M 156 " --> pdb=" O THR M 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.075A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.934A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 3.573A pdb=" N SER B 19 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.652A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.206A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.966A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.130A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.756A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 668 removed outlier: 6.840A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.896A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.623A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.582A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.532A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.605A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.942A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.195A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 236 removed outlier: 4.054A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.219A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.636A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.163A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 3.964A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1182 removed outlier: 6.540A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.913A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 14.69 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8051 1.33 - 1.45: 5583 1.45 - 1.57: 16486 1.57 - 1.69: 247 1.69 - 1.81: 175 Bond restraints: 30542 Sorted by residual: bond pdb=" C ARG C 421 " pdb=" N PRO C 422 " ideal model delta sigma weight residual 1.336 1.396 -0.061 1.23e-02 6.61e+03 2.42e+01 bond pdb=" CA ILE C 773 " pdb=" C ILE C 773 " ideal model delta sigma weight residual 1.524 1.480 0.045 1.05e-02 9.07e+03 1.80e+01 bond pdb=" C VAL C 922 " pdb=" N PRO C 923 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.23e-02 6.61e+03 1.21e+01 bond pdb=" CA ALA A 222 " pdb=" C ALA A 222 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.15e+01 bond pdb=" CA ALA C 634 " pdb=" C ALA C 634 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.35e-02 5.49e+03 1.10e+01 ... (remaining 30537 not shown) Histogram of bond angle deviations from ideal: 97.20 - 106.38: 1660 106.38 - 115.57: 19026 115.57 - 124.75: 20319 124.75 - 133.94: 894 133.94 - 143.13: 7 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.99 103.99 16.00 1.08e+00 8.57e-01 2.20e+02 angle pdb=" N LEU A 225 " pdb=" CA LEU A 225 " pdb=" C LEU A 225 " ideal model delta sigma weight residual 113.37 99.17 14.20 1.38e+00 5.25e-01 1.06e+02 angle pdb=" C ILE C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.84 129.19 -9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 142.39 -15.39 2.40e+00 1.74e-01 4.11e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 106.71 13.89 2.20e+00 2.07e-01 3.98e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 17556 35.43 - 70.86: 755 70.86 - 106.29: 11 106.29 - 141.72: 0 141.72 - 177.15: 5 Dihedral angle restraints: 18327 sinusoidal: 8279 harmonic: 10048 Sorted by residual: dihedral pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual 122.80 138.78 -15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C GLU A 224 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual -122.60 -137.99 15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" CA VAL D 4 " pdb=" C VAL D 4 " pdb=" N ASN D 5 " pdb=" CA ASN D 5 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 18324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4704 0.150 - 0.300: 65 0.300 - 0.450: 3 0.450 - 0.600: 1 0.600 - 0.750: 2 Chirality restraints: 4775 Sorted by residual: chirality pdb=" CA GLU A 224 " pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CB GLU A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU A 221 " pdb=" CB LEU A 221 " pdb=" CD1 LEU A 221 " pdb=" CD2 LEU A 221 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ARG A 223 " pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CB ARG A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 4772 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG M 75 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C ARG M 75 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG M 75 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA M 76 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 56 " -0.031 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR E 56 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR E 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR E 56 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 56 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 21 " 0.039 2.00e-02 2.50e+03 1.65e-02 8.19e+00 pdb=" N9 DG O 21 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 21 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DG O 21 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG O 21 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG O 21 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG O 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG O 21 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG O 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG O 21 " -0.004 2.00e-02 2.50e+03 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 571 2.65 - 3.21: 26564 3.21 - 3.77: 50049 3.77 - 4.34: 63859 4.34 - 4.90: 99898 Nonbonded interactions: 240941 Sorted by model distance: nonbonded pdb=" NH2 ARG F 502 " pdb=" OP2 DT O 23 " model vdw 2.082 2.520 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.099 2.170 nonbonded pdb=" O GLY D 408 " pdb=" NH1 ARG D 414 " model vdw 2.120 2.520 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.126 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.129 2.170 ... (remaining 240936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } 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=0.50 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.310 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 99.490 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 30542 Z= 0.431 Angle : 1.044 18.126 41906 Z= 0.608 Chirality : 0.058 0.750 4775 Planarity : 0.007 0.060 5070 Dihedral : 16.003 177.146 11863 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer: Outliers : 0.65 % Allowed : 5.01 % Favored : 94.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 3488 helix: -1.64 (0.11), residues: 1366 sheet: -2.12 (0.25), residues: 349 loop : -2.50 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP C 70 HIS 0.014 0.003 HIS C 751 PHE 0.042 0.003 PHE D 6 TYR 0.053 0.003 TYR E 56 ARG 0.013 0.001 ARG D 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 3.593 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: A 95 MET cc_start: 0.8782 (ptp) cc_final: 0.8582 (pmm) REVERT: B 191 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8709 (tttp) REVERT: B 226 ASN cc_start: 0.8834 (t160) cc_final: 0.8563 (t0) REVERT: C 202 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (m) REVERT: C 355 MET cc_start: 0.8995 (tmm) cc_final: 0.8686 (tmm) REVERT: C 396 MET cc_start: 0.9463 (tmt) cc_final: 0.8889 (tmm) REVERT: C 607 MET cc_start: 0.8781 (mtt) cc_final: 0.8495 (mtm) REVERT: C 611 MET cc_start: 0.9310 (mtm) cc_final: 0.8940 (ptp) REVERT: C 630 MET cc_start: 0.8955 (mmm) cc_final: 0.8667 (mmm) REVERT: C 733 ASP cc_start: 0.8636 (m-30) cc_final: 0.8399 (p0) REVERT: C 1038 ASP cc_start: 0.9185 (m-30) cc_final: 0.8738 (p0) REVERT: C 1088 LEU cc_start: 0.9545 (mt) cc_final: 0.9286 (pp) REVERT: C 1119 GLU cc_start: 0.8715 (tp30) cc_final: 0.8385 (tp30) REVERT: D 114 LEU cc_start: 0.9559 (mt) cc_final: 0.9176 (mt) REVERT: D 256 MET cc_start: 0.8351 (ttm) cc_final: 0.7784 (ttm) REVERT: D 373 MET cc_start: 0.8987 (mtp) cc_final: 0.8760 (mtp) REVERT: D 491 ILE cc_start: 0.9579 (mt) cc_final: 0.9363 (pt) REVERT: D 541 MET cc_start: 0.8606 (mtp) cc_final: 0.8069 (mtp) REVERT: D 1112 MET cc_start: 0.7305 (mmm) cc_final: 0.6858 (mmm) REVERT: E 41 ASP cc_start: 0.8792 (m-30) cc_final: 0.8444 (m-30) REVERT: E 42 GLU cc_start: 0.9539 (mt-10) cc_final: 0.8750 (tp30) REVERT: E 66 ASP cc_start: 0.9148 (m-30) cc_final: 0.8946 (t0) REVERT: E 105 GLU cc_start: 0.8676 (pt0) cc_final: 0.8440 (pt0) outliers start: 19 outliers final: 7 residues processed: 237 average time/residue: 0.4645 time to fit residues: 170.5803 Evaluate side-chains 130 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 578 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 61 HIS B 124 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 226 ASN C 81 ASN C 141 ASN C 143 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 388 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN C 729 HIS C 875 GLN C 920 HIS C1062 GLN C1066 GLN D 239 ASN D 307 ASN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 564 ASN D 687 GLN D 693 GLN D 771 ASN D 797 ASN D1139 GLN D1145 GLN D1190 ASN E 65 ASN E 69 ASN E 88 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30542 Z= 0.233 Angle : 0.645 12.228 41906 Z= 0.343 Chirality : 0.042 0.156 4775 Planarity : 0.005 0.054 5070 Dihedral : 19.416 175.168 5217 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 1.78 % Allowed : 7.99 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -1.58 (0.14), residues: 3488 helix: 0.14 (0.13), residues: 1397 sheet: -1.45 (0.28), residues: 323 loop : -2.00 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 70 HIS 0.004 0.001 HIS D 748 PHE 0.021 0.001 PHE D 6 TYR 0.035 0.002 TYR E 56 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8834 (ttm) cc_final: 0.8366 (tmm) REVERT: B 1 MET cc_start: 0.8348 (tpp) cc_final: 0.7838 (tpp) REVERT: B 191 LYS cc_start: 0.9235 (ttpt) cc_final: 0.9033 (ttpp) REVERT: B 226 ASN cc_start: 0.8817 (t0) cc_final: 0.8523 (t0) REVERT: C 103 MET cc_start: 0.9462 (ptp) cc_final: 0.8836 (ppp) REVERT: C 122 CYS cc_start: 0.9387 (m) cc_final: 0.9095 (m) REVERT: C 355 MET cc_start: 0.8920 (tmm) cc_final: 0.8678 (tmm) REVERT: C 393 MET cc_start: 0.9344 (tpp) cc_final: 0.8793 (tpp) REVERT: C 396 MET cc_start: 0.9425 (tmt) cc_final: 0.9104 (tmm) REVERT: C 404 MET cc_start: 0.8582 (ptt) cc_final: 0.8227 (ptp) REVERT: C 412 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8684 (mm) REVERT: C 561 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8716 (p) REVERT: C 586 MET cc_start: 0.8983 (ppp) cc_final: 0.8221 (ppp) REVERT: C 607 MET cc_start: 0.8834 (mtt) cc_final: 0.8491 (mtm) REVERT: C 611 MET cc_start: 0.9252 (mtm) cc_final: 0.8822 (ptp) REVERT: C 630 MET cc_start: 0.9036 (mmm) cc_final: 0.8789 (mmp) REVERT: C 661 MET cc_start: 0.9012 (tpt) cc_final: 0.8747 (tpt) REVERT: C 1038 ASP cc_start: 0.9196 (m-30) cc_final: 0.8808 (p0) REVERT: C 1076 MET cc_start: 0.9195 (mmm) cc_final: 0.8985 (mmm) REVERT: C 1119 GLU cc_start: 0.8676 (tp30) cc_final: 0.8229 (tp30) REVERT: D 114 LEU cc_start: 0.9578 (mt) cc_final: 0.9233 (mt) REVERT: D 256 MET cc_start: 0.8300 (ttm) cc_final: 0.7922 (ttm) REVERT: D 373 MET cc_start: 0.8937 (mtp) cc_final: 0.8687 (mtp) REVERT: D 491 ILE cc_start: 0.9597 (mt) cc_final: 0.9353 (pt) REVERT: D 516 LEU cc_start: 0.9377 (mt) cc_final: 0.9095 (mt) REVERT: D 541 MET cc_start: 0.8252 (mtp) cc_final: 0.7953 (mtp) REVERT: D 706 MET cc_start: 0.9251 (mmm) cc_final: 0.8891 (mmm) REVERT: D 733 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8418 (tmm) REVERT: D 983 MET cc_start: 0.8369 (tpp) cc_final: 0.8130 (tpp) REVERT: D 1112 MET cc_start: 0.7806 (mmm) cc_final: 0.7390 (mmm) REVERT: D 1161 MET cc_start: 0.9071 (mtp) cc_final: 0.8481 (mtp) REVERT: E 41 ASP cc_start: 0.8728 (m-30) cc_final: 0.8463 (m-30) REVERT: E 42 GLU cc_start: 0.9581 (mt-10) cc_final: 0.8861 (tp30) REVERT: E 78 TYR cc_start: 0.8251 (m-10) cc_final: 0.7973 (m-10) REVERT: F 281 MET cc_start: 0.9113 (ptm) cc_final: 0.8832 (ptp) REVERT: F 282 MET cc_start: 0.9403 (mmm) cc_final: 0.9165 (mmm) REVERT: J 86 LEU cc_start: 0.9816 (OUTLIER) cc_final: 0.9554 (pp) REVERT: M 11 TYR cc_start: 0.9154 (t80) cc_final: 0.8311 (t80) outliers start: 52 outliers final: 16 residues processed: 181 average time/residue: 0.4018 time to fit residues: 120.7950 Evaluate side-chains 137 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 351 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 261 optimal weight: 0.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 30542 Z= 0.305 Angle : 0.661 11.194 41906 Z= 0.348 Chirality : 0.042 0.163 4775 Planarity : 0.005 0.055 5070 Dihedral : 19.257 175.796 5208 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.25 % Favored : 93.72 % Rotamer: Outliers : 1.92 % Allowed : 9.22 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.99 (0.14), residues: 3488 helix: 0.78 (0.14), residues: 1410 sheet: -1.41 (0.27), residues: 344 loop : -1.75 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 70 HIS 0.006 0.001 HIS D1150 PHE 0.019 0.002 PHE D 6 TYR 0.036 0.002 TYR E 56 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8861 (ttm) cc_final: 0.8498 (tmm) REVERT: B 1 MET cc_start: 0.8490 (tpp) cc_final: 0.7988 (tpp) REVERT: B 70 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9061 (ptpp) REVERT: B 173 LYS cc_start: 0.9121 (tptt) cc_final: 0.8847 (tptp) REVERT: B 226 ASN cc_start: 0.8751 (t0) cc_final: 0.8536 (t0) REVERT: C 103 MET cc_start: 0.9426 (ptp) cc_final: 0.8878 (ppp) REVERT: C 122 CYS cc_start: 0.9291 (m) cc_final: 0.9016 (m) REVERT: C 355 MET cc_start: 0.8910 (tmm) cc_final: 0.8617 (tmm) REVERT: C 393 MET cc_start: 0.9393 (tpp) cc_final: 0.9077 (mmm) REVERT: C 404 MET cc_start: 0.8584 (ptt) cc_final: 0.8231 (ptp) REVERT: C 586 MET cc_start: 0.9114 (ppp) cc_final: 0.7879 (ppp) REVERT: C 607 MET cc_start: 0.8869 (mtt) cc_final: 0.8509 (mtm) REVERT: C 611 MET cc_start: 0.9291 (mtm) cc_final: 0.8752 (ptp) REVERT: C 630 MET cc_start: 0.9176 (mmm) cc_final: 0.8966 (mmp) REVERT: C 661 MET cc_start: 0.9030 (tpt) cc_final: 0.8653 (tpt) REVERT: C 1038 ASP cc_start: 0.9145 (m-30) cc_final: 0.8900 (p0) REVERT: C 1076 MET cc_start: 0.9335 (mmm) cc_final: 0.8756 (mmm) REVERT: C 1119 GLU cc_start: 0.8744 (tp30) cc_final: 0.8285 (tp30) REVERT: D 155 MET cc_start: 0.8671 (tpt) cc_final: 0.8398 (tmm) REVERT: D 229 LEU cc_start: 0.9408 (mt) cc_final: 0.9062 (mt) REVERT: D 256 MET cc_start: 0.8318 (ttm) cc_final: 0.7893 (ttm) REVERT: D 491 ILE cc_start: 0.9583 (mt) cc_final: 0.9298 (pt) REVERT: D 516 LEU cc_start: 0.9427 (mt) cc_final: 0.9122 (mt) REVERT: D 541 MET cc_start: 0.8035 (mtp) cc_final: 0.7787 (mtp) REVERT: D 1112 MET cc_start: 0.7771 (mmm) cc_final: 0.7282 (mmm) REVERT: E 41 ASP cc_start: 0.8764 (m-30) cc_final: 0.8538 (m-30) REVERT: E 42 GLU cc_start: 0.9585 (mt-10) cc_final: 0.8995 (tp30) REVERT: J 84 MET cc_start: 0.9031 (mpp) cc_final: 0.8738 (mpp) REVERT: M 11 TYR cc_start: 0.9141 (t80) cc_final: 0.8229 (t80) REVERT: M 55 TYR cc_start: 0.8098 (m-80) cc_final: 0.7848 (m-80) outliers start: 56 outliers final: 33 residues processed: 169 average time/residue: 0.3908 time to fit residues: 110.6850 Evaluate side-chains 145 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 326 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30542 Z= 0.226 Angle : 0.600 9.389 41906 Z= 0.314 Chirality : 0.041 0.156 4775 Planarity : 0.004 0.053 5070 Dihedral : 19.096 175.295 5207 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 2.19 % Allowed : 9.74 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.61 (0.14), residues: 3488 helix: 1.12 (0.14), residues: 1417 sheet: -1.12 (0.27), residues: 340 loop : -1.60 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 70 HIS 0.005 0.001 HIS D1150 PHE 0.019 0.001 PHE D 6 TYR 0.030 0.001 TYR E 56 ARG 0.007 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 117 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8893 (ttm) cc_final: 0.8551 (tmm) REVERT: B 1 MET cc_start: 0.8496 (tpp) cc_final: 0.7951 (tpp) REVERT: B 177 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8160 (ptmm) REVERT: B 226 ASN cc_start: 0.8782 (t0) cc_final: 0.8570 (t0) REVERT: C 103 MET cc_start: 0.9334 (ptp) cc_final: 0.8692 (ppp) REVERT: C 122 CYS cc_start: 0.9268 (m) cc_final: 0.8983 (m) REVERT: C 355 MET cc_start: 0.8828 (tmm) cc_final: 0.8559 (tmm) REVERT: C 393 MET cc_start: 0.9437 (tpp) cc_final: 0.9177 (mmm) REVERT: C 404 MET cc_start: 0.8555 (ptt) cc_final: 0.8290 (ptp) REVERT: C 412 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8903 (mm) REVERT: C 561 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 586 MET cc_start: 0.9263 (ppp) cc_final: 0.8159 (ppp) REVERT: C 607 MET cc_start: 0.8857 (mtt) cc_final: 0.8561 (mtm) REVERT: C 611 MET cc_start: 0.9269 (mtm) cc_final: 0.8811 (mtp) REVERT: C 630 MET cc_start: 0.9149 (mmm) cc_final: 0.8853 (mmm) REVERT: C 661 MET cc_start: 0.8983 (tpt) cc_final: 0.8615 (tpt) REVERT: C 784 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9164 (pp) REVERT: C 907 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8886 (tm) REVERT: C 1038 ASP cc_start: 0.9142 (m-30) cc_final: 0.8938 (p0) REVERT: C 1076 MET cc_start: 0.9399 (mmm) cc_final: 0.8837 (mmm) REVERT: C 1119 GLU cc_start: 0.8737 (tp30) cc_final: 0.8281 (tp30) REVERT: D 155 MET cc_start: 0.8625 (tpt) cc_final: 0.8381 (tmm) REVERT: D 229 LEU cc_start: 0.9475 (mt) cc_final: 0.9195 (mt) REVERT: D 256 MET cc_start: 0.8342 (ttm) cc_final: 0.7950 (ttm) REVERT: D 373 MET cc_start: 0.8764 (mtp) cc_final: 0.8439 (ptp) REVERT: D 581 MET cc_start: 0.8760 (pmm) cc_final: 0.8348 (pmm) REVERT: D 706 MET cc_start: 0.9256 (mmm) cc_final: 0.8935 (mmm) REVERT: D 983 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7692 (tpp) REVERT: D 1112 MET cc_start: 0.7638 (mmm) cc_final: 0.7391 (mmm) REVERT: E 41 ASP cc_start: 0.8763 (m-30) cc_final: 0.8552 (m-30) REVERT: E 42 GLU cc_start: 0.9602 (mt-10) cc_final: 0.8914 (tp30) REVERT: F 498 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8178 (t) REVERT: J 60 MET cc_start: 0.8112 (ppp) cc_final: 0.6890 (ppp) REVERT: J 86 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9585 (pp) REVERT: M 11 TYR cc_start: 0.9121 (t80) cc_final: 0.8263 (t80) outliers start: 64 outliers final: 37 residues processed: 172 average time/residue: 0.3875 time to fit residues: 111.8207 Evaluate side-chains 154 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 257 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30542 Z= 0.257 Angle : 0.612 11.040 41906 Z= 0.319 Chirality : 0.041 0.277 4775 Planarity : 0.004 0.055 5070 Dihedral : 19.013 175.827 5207 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.11 % Favored : 93.86 % Rotamer: Outliers : 2.37 % Allowed : 10.11 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.38 (0.14), residues: 3488 helix: 1.33 (0.14), residues: 1413 sheet: -0.88 (0.28), residues: 338 loop : -1.52 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 70 HIS 0.006 0.001 HIS D1150 PHE 0.016 0.001 PHE D 6 TYR 0.028 0.001 TYR E 56 ARG 0.006 0.000 ARG F 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 111 time to evaluate : 3.428 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: A 123 MET cc_start: 0.8890 (ttm) cc_final: 0.8592 (tmm) REVERT: B 1 MET cc_start: 0.8536 (tpp) cc_final: 0.7942 (tpp) REVERT: B 70 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9092 (ptpp) REVERT: B 173 LYS cc_start: 0.9050 (tptp) cc_final: 0.8688 (tptp) REVERT: B 177 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8124 (ptmm) REVERT: C 103 MET cc_start: 0.9341 (ptp) cc_final: 0.8739 (ppp) REVERT: C 122 CYS cc_start: 0.9261 (m) cc_final: 0.9003 (m) REVERT: C 355 MET cc_start: 0.8814 (tmm) cc_final: 0.8514 (tmm) REVERT: C 393 MET cc_start: 0.9438 (tpp) cc_final: 0.9170 (mmm) REVERT: C 404 MET cc_start: 0.8664 (ptt) cc_final: 0.8421 (ptp) REVERT: C 443 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8403 (p0) REVERT: C 586 MET cc_start: 0.9319 (ppp) cc_final: 0.8258 (ppp) REVERT: C 607 MET cc_start: 0.8853 (mtt) cc_final: 0.8559 (mtm) REVERT: C 611 MET cc_start: 0.9270 (mtm) cc_final: 0.8840 (mtp) REVERT: C 630 MET cc_start: 0.9160 (mmm) cc_final: 0.8871 (mmm) REVERT: C 661 MET cc_start: 0.8998 (tpt) cc_final: 0.8581 (tpt) REVERT: C 784 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9108 (pp) REVERT: C 907 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8919 (tm) REVERT: C 1076 MET cc_start: 0.9415 (mmm) cc_final: 0.8875 (mmm) REVERT: C 1119 GLU cc_start: 0.8771 (tp30) cc_final: 0.8330 (tp30) REVERT: D 155 MET cc_start: 0.8636 (tpt) cc_final: 0.8427 (tmm) REVERT: D 229 LEU cc_start: 0.9475 (mt) cc_final: 0.9064 (mt) REVERT: D 256 MET cc_start: 0.8201 (ttm) cc_final: 0.7524 (mtp) REVERT: D 373 MET cc_start: 0.8753 (mtp) cc_final: 0.8442 (ptp) REVERT: D 516 LEU cc_start: 0.9498 (mt) cc_final: 0.8999 (pt) REVERT: D 576 MET cc_start: 0.8940 (tpp) cc_final: 0.8726 (tpp) REVERT: D 581 MET cc_start: 0.8933 (pmm) cc_final: 0.8434 (pmm) REVERT: D 983 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7671 (tpp) REVERT: D 1112 MET cc_start: 0.7730 (mmm) cc_final: 0.7448 (mmm) REVERT: E 41 ASP cc_start: 0.8771 (m-30) cc_final: 0.8566 (m-30) REVERT: E 42 GLU cc_start: 0.9571 (mt-10) cc_final: 0.8902 (tp30) REVERT: J 60 MET cc_start: 0.8368 (ppp) cc_final: 0.7269 (ppp) REVERT: J 86 LEU cc_start: 0.9791 (OUTLIER) cc_final: 0.9590 (pp) REVERT: M 11 TYR cc_start: 0.9102 (t80) cc_final: 0.8246 (t80) outliers start: 69 outliers final: 44 residues processed: 172 average time/residue: 0.3959 time to fit residues: 114.2025 Evaluate side-chains 155 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 160 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30542 Z= 0.166 Angle : 0.583 13.299 41906 Z= 0.299 Chirality : 0.041 0.186 4775 Planarity : 0.004 0.053 5070 Dihedral : 18.894 175.981 5207 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 2.16 % Allowed : 10.49 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.14 (0.15), residues: 3488 helix: 1.61 (0.14), residues: 1400 sheet: -0.71 (0.28), residues: 341 loop : -1.44 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 PHE 0.016 0.001 PHE D 6 TYR 0.023 0.001 TYR E 67 ARG 0.004 0.000 ARG M 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 117 time to evaluate : 3.406 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: A 123 MET cc_start: 0.8917 (ttm) cc_final: 0.8544 (tmm) REVERT: B 1 MET cc_start: 0.8470 (tpp) cc_final: 0.7947 (tpp) REVERT: B 70 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9055 (pttm) REVERT: B 173 LYS cc_start: 0.9011 (tptp) cc_final: 0.8792 (tptp) REVERT: B 177 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8107 (ptmm) REVERT: C 103 MET cc_start: 0.9308 (ptp) cc_final: 0.8751 (ppp) REVERT: C 159 MET cc_start: 0.9279 (tpp) cc_final: 0.8785 (mmm) REVERT: C 355 MET cc_start: 0.8817 (tmm) cc_final: 0.8565 (tmm) REVERT: C 393 MET cc_start: 0.9433 (tpp) cc_final: 0.9157 (mmm) REVERT: C 404 MET cc_start: 0.8685 (ptt) cc_final: 0.8428 (ptp) REVERT: C 443 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8012 (p0) REVERT: C 586 MET cc_start: 0.9324 (ppp) cc_final: 0.8258 (ppp) REVERT: C 607 MET cc_start: 0.8837 (mtt) cc_final: 0.8547 (mtm) REVERT: C 611 MET cc_start: 0.9257 (mtm) cc_final: 0.8838 (mtp) REVERT: C 630 MET cc_start: 0.9074 (mmm) cc_final: 0.8831 (mmm) REVERT: C 661 MET cc_start: 0.8968 (tpt) cc_final: 0.8557 (tpt) REVERT: C 784 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9087 (pp) REVERT: C 907 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8889 (tm) REVERT: C 1071 MET cc_start: 0.9279 (mtp) cc_final: 0.9035 (mtp) REVERT: C 1076 MET cc_start: 0.9386 (mmm) cc_final: 0.8875 (mmm) REVERT: C 1119 GLU cc_start: 0.8744 (tp30) cc_final: 0.8325 (tp30) REVERT: D 155 MET cc_start: 0.8607 (tpt) cc_final: 0.8402 (tmm) REVERT: D 229 LEU cc_start: 0.9450 (mt) cc_final: 0.9000 (mt) REVERT: D 256 MET cc_start: 0.8160 (ttm) cc_final: 0.7830 (ttm) REVERT: D 373 MET cc_start: 0.8784 (mtp) cc_final: 0.8504 (ptp) REVERT: D 516 LEU cc_start: 0.9488 (mt) cc_final: 0.8970 (pt) REVERT: D 581 MET cc_start: 0.8869 (pmm) cc_final: 0.8412 (pmm) REVERT: D 706 MET cc_start: 0.9217 (mmm) cc_final: 0.8894 (mmm) REVERT: D 983 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7544 (tpp) REVERT: D 991 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8661 (tp) REVERT: D 1112 MET cc_start: 0.7613 (mmm) cc_final: 0.7375 (mmm) REVERT: E 41 ASP cc_start: 0.8863 (m-30) cc_final: 0.8636 (m-30) REVERT: E 42 GLU cc_start: 0.9550 (mt-10) cc_final: 0.8703 (tp30) REVERT: F 282 MET cc_start: 0.9173 (mmm) cc_final: 0.8794 (mmp) REVERT: J 60 MET cc_start: 0.8435 (ppp) cc_final: 0.7196 (ppp) REVERT: M 11 TYR cc_start: 0.9069 (t80) cc_final: 0.8332 (t80) outliers start: 63 outliers final: 44 residues processed: 174 average time/residue: 0.4037 time to fit residues: 116.6938 Evaluate side-chains 157 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30542 Z= 0.251 Angle : 0.608 11.156 41906 Z= 0.313 Chirality : 0.041 0.176 4775 Planarity : 0.004 0.061 5070 Dihedral : 18.918 175.731 5207 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 2.33 % Allowed : 10.59 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.09 (0.15), residues: 3488 helix: 1.64 (0.14), residues: 1403 sheet: -0.67 (0.28), residues: 348 loop : -1.41 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 70 HIS 0.005 0.001 HIS D1150 PHE 0.017 0.001 PHE C 61 TYR 0.024 0.001 TYR E 56 ARG 0.005 0.000 ARG M 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 107 time to evaluate : 3.628 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: A 123 MET cc_start: 0.8915 (ttm) cc_final: 0.8572 (tmm) REVERT: B 1 MET cc_start: 0.8583 (tpp) cc_final: 0.7986 (tpp) REVERT: B 70 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9050 (pttm) REVERT: B 173 LYS cc_start: 0.9010 (tptp) cc_final: 0.8774 (tptp) REVERT: C 103 MET cc_start: 0.9328 (ptp) cc_final: 0.8766 (ppp) REVERT: C 159 MET cc_start: 0.9302 (tpp) cc_final: 0.8789 (mmm) REVERT: C 355 MET cc_start: 0.8837 (tmm) cc_final: 0.8525 (tmm) REVERT: C 393 MET cc_start: 0.9442 (tpp) cc_final: 0.9164 (mmm) REVERT: C 404 MET cc_start: 0.8722 (ptt) cc_final: 0.8358 (ptp) REVERT: C 443 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8248 (p0) REVERT: C 586 MET cc_start: 0.9343 (ppp) cc_final: 0.8316 (ppp) REVERT: C 607 MET cc_start: 0.8856 (mtt) cc_final: 0.8572 (mtm) REVERT: C 611 MET cc_start: 0.9273 (mtm) cc_final: 0.8848 (mtp) REVERT: C 630 MET cc_start: 0.9107 (mmm) cc_final: 0.8890 (mmp) REVERT: C 661 MET cc_start: 0.8982 (tpt) cc_final: 0.8557 (tpt) REVERT: C 784 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9103 (pp) REVERT: C 907 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8930 (tm) REVERT: C 1076 MET cc_start: 0.9407 (mmm) cc_final: 0.8878 (mmm) REVERT: C 1119 GLU cc_start: 0.8774 (tp30) cc_final: 0.8323 (tp30) REVERT: D 155 MET cc_start: 0.8606 (tpt) cc_final: 0.8398 (tmm) REVERT: D 229 LEU cc_start: 0.9474 (mt) cc_final: 0.9082 (mt) REVERT: D 256 MET cc_start: 0.8178 (ttm) cc_final: 0.7487 (mtp) REVERT: D 373 MET cc_start: 0.8777 (mtp) cc_final: 0.8503 (ptp) REVERT: D 516 LEU cc_start: 0.9449 (mt) cc_final: 0.9020 (pt) REVERT: D 581 MET cc_start: 0.8914 (pmm) cc_final: 0.8453 (pmm) REVERT: D 706 MET cc_start: 0.9218 (mmm) cc_final: 0.8894 (mmm) REVERT: D 975 CYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8852 (p) REVERT: D 983 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7643 (tpp) REVERT: D 991 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8720 (tp) REVERT: D 1112 MET cc_start: 0.7633 (mmm) cc_final: 0.7361 (mmp) REVERT: E 41 ASP cc_start: 0.8878 (m-30) cc_final: 0.8660 (m-30) REVERT: E 42 GLU cc_start: 0.9558 (mt-10) cc_final: 0.8919 (tp30) REVERT: F 282 MET cc_start: 0.9232 (mmm) cc_final: 0.8903 (mmm) REVERT: J 60 MET cc_start: 0.8482 (ppp) cc_final: 0.7297 (ppp) REVERT: M 11 TYR cc_start: 0.9075 (t80) cc_final: 0.8203 (t80) outliers start: 68 outliers final: 49 residues processed: 169 average time/residue: 0.4140 time to fit residues: 115.9286 Evaluate side-chains 162 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 106 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30542 Z= 0.204 Angle : 0.594 11.447 41906 Z= 0.304 Chirality : 0.040 0.217 4775 Planarity : 0.004 0.055 5070 Dihedral : 18.890 176.281 5207 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.19 % Allowed : 10.94 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: 0.02 (0.15), residues: 3488 helix: 1.74 (0.14), residues: 1397 sheet: -0.57 (0.28), residues: 339 loop : -1.35 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 70 HIS 0.005 0.001 HIS D1150 PHE 0.021 0.001 PHE C 61 TYR 0.022 0.001 TYR E 56 ARG 0.005 0.000 ARG M 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 108 time to evaluate : 3.391 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: A 123 MET cc_start: 0.8921 (ttm) cc_final: 0.8560 (tmm) REVERT: B 1 MET cc_start: 0.8591 (tpp) cc_final: 0.8000 (tpp) REVERT: B 70 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9090 (pttm) REVERT: B 173 LYS cc_start: 0.9023 (tptp) cc_final: 0.8791 (tptp) REVERT: C 103 MET cc_start: 0.9300 (ptp) cc_final: 0.8779 (ppp) REVERT: C 355 MET cc_start: 0.8867 (tmm) cc_final: 0.8553 (tmm) REVERT: C 393 MET cc_start: 0.9442 (tpp) cc_final: 0.9153 (mmm) REVERT: C 404 MET cc_start: 0.8728 (ptt) cc_final: 0.8356 (ptp) REVERT: C 443 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8200 (p0) REVERT: C 586 MET cc_start: 0.9342 (ppp) cc_final: 0.8308 (ppp) REVERT: C 607 MET cc_start: 0.8848 (mtt) cc_final: 0.8567 (mtm) REVERT: C 611 MET cc_start: 0.9263 (mtm) cc_final: 0.8849 (mtp) REVERT: C 630 MET cc_start: 0.9072 (mmm) cc_final: 0.8868 (mmm) REVERT: C 661 MET cc_start: 0.8969 (tpt) cc_final: 0.8547 (tpt) REVERT: C 784 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9072 (pp) REVERT: C 907 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8901 (tm) REVERT: C 1076 MET cc_start: 0.9405 (mmm) cc_final: 0.8876 (mmm) REVERT: C 1119 GLU cc_start: 0.8770 (tp30) cc_final: 0.8335 (tp30) REVERT: D 155 MET cc_start: 0.8599 (tpt) cc_final: 0.8393 (tmm) REVERT: D 229 LEU cc_start: 0.9475 (mt) cc_final: 0.9121 (mt) REVERT: D 256 MET cc_start: 0.8148 (ttm) cc_final: 0.7474 (mtp) REVERT: D 373 MET cc_start: 0.8762 (mtp) cc_final: 0.8490 (ptp) REVERT: D 516 LEU cc_start: 0.9444 (mt) cc_final: 0.9034 (pt) REVERT: D 574 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9296 (mm) REVERT: D 581 MET cc_start: 0.8883 (pmm) cc_final: 0.8418 (pmm) REVERT: D 706 MET cc_start: 0.9204 (mmm) cc_final: 0.8878 (mmm) REVERT: D 975 CYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8847 (p) REVERT: D 983 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7615 (tpp) REVERT: D 991 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8719 (tp) REVERT: D 1112 MET cc_start: 0.7620 (mmm) cc_final: 0.7278 (mmp) REVERT: E 42 GLU cc_start: 0.9558 (mt-10) cc_final: 0.8915 (tp30) REVERT: F 282 MET cc_start: 0.9269 (mmm) cc_final: 0.8921 (mmp) REVERT: J 60 MET cc_start: 0.8523 (ppp) cc_final: 0.7350 (ppp) REVERT: M 11 TYR cc_start: 0.9070 (t80) cc_final: 0.8241 (t80) outliers start: 64 outliers final: 49 residues processed: 165 average time/residue: 0.3977 time to fit residues: 110.1992 Evaluate side-chains 163 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 106 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 321 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 320 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30542 Z= 0.212 Angle : 0.595 10.703 41906 Z= 0.304 Chirality : 0.040 0.205 4775 Planarity : 0.004 0.057 5070 Dihedral : 18.896 176.578 5207 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.33 % Allowed : 10.73 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: 0.06 (0.15), residues: 3488 helix: 1.74 (0.14), residues: 1414 sheet: -0.50 (0.27), residues: 360 loop : -1.35 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 70 HIS 0.005 0.001 HIS D1150 PHE 0.018 0.001 PHE C 61 TYR 0.032 0.001 TYR E 67 ARG 0.005 0.000 ARG M 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 109 time to evaluate : 3.373 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 123 MET cc_start: 0.8931 (ttm) cc_final: 0.8564 (tmm) REVERT: B 1 MET cc_start: 0.8609 (tpp) cc_final: 0.8009 (tpp) REVERT: B 70 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9173 (pttm) REVERT: C 77 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (mtm-85) REVERT: C 103 MET cc_start: 0.9283 (ptp) cc_final: 0.8787 (ppp) REVERT: C 282 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5554 (pmm-80) REVERT: C 355 MET cc_start: 0.8870 (tmm) cc_final: 0.8553 (tmm) REVERT: C 393 MET cc_start: 0.9451 (tpp) cc_final: 0.9163 (mmm) REVERT: C 404 MET cc_start: 0.8735 (ptt) cc_final: 0.8369 (ptp) REVERT: C 443 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8219 (p0) REVERT: C 586 MET cc_start: 0.9354 (ppp) cc_final: 0.8325 (ppp) REVERT: C 607 MET cc_start: 0.8845 (mtt) cc_final: 0.8566 (mtm) REVERT: C 611 MET cc_start: 0.9255 (mtm) cc_final: 0.8846 (mtp) REVERT: C 630 MET cc_start: 0.9009 (mmm) cc_final: 0.8805 (mmp) REVERT: C 661 MET cc_start: 0.8977 (tpt) cc_final: 0.8552 (tpt) REVERT: C 784 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9074 (pp) REVERT: C 907 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8931 (tm) REVERT: C 1051 MET cc_start: 0.8877 (tpp) cc_final: 0.8223 (tpp) REVERT: C 1076 MET cc_start: 0.9404 (mmm) cc_final: 0.8885 (mmm) REVERT: C 1119 GLU cc_start: 0.8774 (tp30) cc_final: 0.8343 (tp30) REVERT: D 155 MET cc_start: 0.8594 (tpt) cc_final: 0.8391 (tmm) REVERT: D 229 LEU cc_start: 0.9481 (mt) cc_final: 0.9148 (mt) REVERT: D 256 MET cc_start: 0.8162 (ttm) cc_final: 0.7477 (mtp) REVERT: D 373 MET cc_start: 0.8757 (mtp) cc_final: 0.8483 (ptp) REVERT: D 447 MET cc_start: 0.9133 (ttp) cc_final: 0.8838 (ptm) REVERT: D 516 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9051 (pt) REVERT: D 574 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9298 (mm) REVERT: D 581 MET cc_start: 0.8889 (pmm) cc_final: 0.8425 (pmm) REVERT: D 975 CYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8816 (p) REVERT: D 991 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (tp) REVERT: D 1012 MET cc_start: 0.8645 (ppp) cc_final: 0.8419 (ppp) REVERT: D 1112 MET cc_start: 0.7707 (mmm) cc_final: 0.7333 (mmp) REVERT: E 41 ASP cc_start: 0.8989 (m-30) cc_final: 0.8701 (m-30) REVERT: E 42 GLU cc_start: 0.9548 (mt-10) cc_final: 0.8928 (tp30) REVERT: F 282 MET cc_start: 0.9299 (mmm) cc_final: 0.8953 (mmm) REVERT: J 60 MET cc_start: 0.8504 (ppp) cc_final: 0.7248 (ppp) REVERT: M 11 TYR cc_start: 0.9069 (t80) cc_final: 0.8218 (t80) outliers start: 68 outliers final: 50 residues processed: 170 average time/residue: 0.4046 time to fit residues: 113.5877 Evaluate side-chains 168 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 356 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 284 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 174 optimal weight: 40.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30542 Z= 0.310 Angle : 0.653 12.765 41906 Z= 0.335 Chirality : 0.041 0.176 4775 Planarity : 0.004 0.070 5070 Dihedral : 18.959 177.244 5207 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 2.19 % Allowed : 10.83 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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 (0.15), residues: 3488 helix: 1.62 (0.14), residues: 1416 sheet: -0.67 (0.27), residues: 370 loop : -1.36 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 243 HIS 0.007 0.001 HIS D1150 PHE 0.019 0.001 PHE C 61 TYR 0.025 0.002 TYR E 56 ARG 0.007 0.000 ARG F 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 107 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8596 (tpp) cc_final: 0.7949 (tpp) REVERT: B 70 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9056 (pttm) REVERT: B 124 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.9154 (t70) REVERT: B 173 LYS cc_start: 0.9019 (tptp) cc_final: 0.8693 (tptp) REVERT: B 177 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8343 (ptmm) REVERT: C 77 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7929 (mtm-85) REVERT: C 103 MET cc_start: 0.9313 (ptp) cc_final: 0.8786 (ppp) REVERT: C 195 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 282 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6151 (pmm-80) REVERT: C 355 MET cc_start: 0.8842 (tmm) cc_final: 0.8528 (tmm) REVERT: C 393 MET cc_start: 0.9453 (tpp) cc_final: 0.9163 (mmm) REVERT: C 404 MET cc_start: 0.8744 (ptt) cc_final: 0.8419 (ptt) REVERT: C 443 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8345 (p0) REVERT: C 586 MET cc_start: 0.9341 (ppp) cc_final: 0.8322 (ppp) REVERT: C 607 MET cc_start: 0.8861 (mtt) cc_final: 0.8570 (mtm) REVERT: C 611 MET cc_start: 0.9274 (mtm) cc_final: 0.8875 (mtp) REVERT: C 784 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9123 (pp) REVERT: C 907 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8956 (tm) REVERT: C 926 MET cc_start: 0.9157 (tpp) cc_final: 0.8689 (tpp) REVERT: C 1119 GLU cc_start: 0.8727 (tp30) cc_final: 0.8362 (tp30) REVERT: D 229 LEU cc_start: 0.9504 (mt) cc_final: 0.9108 (mt) REVERT: D 256 MET cc_start: 0.8148 (ttm) cc_final: 0.7444 (mtp) REVERT: D 373 MET cc_start: 0.8774 (mtp) cc_final: 0.8506 (ptp) REVERT: D 516 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9123 (pp) REVERT: D 574 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9295 (mm) REVERT: D 581 MET cc_start: 0.8945 (pmm) cc_final: 0.8491 (pmm) REVERT: D 975 CYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 991 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8800 (tp) REVERT: E 41 ASP cc_start: 0.8998 (m-30) cc_final: 0.8765 (m-30) REVERT: E 42 GLU cc_start: 0.9560 (mt-10) cc_final: 0.8872 (tp30) REVERT: F 282 MET cc_start: 0.9450 (mmm) cc_final: 0.8953 (mmm) REVERT: J 60 MET cc_start: 0.8481 (ppp) cc_final: 0.7322 (ppp) REVERT: M 11 TYR cc_start: 0.9061 (t80) cc_final: 0.8154 (t80) outliers start: 64 outliers final: 49 residues processed: 164 average time/residue: 0.4075 time to fit residues: 110.2923 Evaluate side-chains 168 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 107 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.035549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.026202 restraints weight = 260355.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.027035 restraints weight = 143480.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027596 restraints weight = 96624.242| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30542 Z= 0.345 Angle : 0.680 13.310 41906 Z= 0.349 Chirality : 0.042 0.180 4775 Planarity : 0.004 0.071 5070 Dihedral : 19.026 177.541 5207 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Rotamer: Outliers : 2.23 % Allowed : 10.83 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % 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: -0.17 (0.15), residues: 3488 helix: 1.47 (0.14), residues: 1416 sheet: -0.72 (0.27), residues: 370 loop : -1.38 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 243 HIS 0.007 0.001 HIS B 124 PHE 0.020 0.002 PHE C 61 TYR 0.026 0.002 TYR E 56 ARG 0.006 0.000 ARG M 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4497.54 seconds wall clock time: 83 minutes 18.31 seconds (4998.31 seconds total)