Starting phenix.real_space_refine on Sat Aug 8 20:47:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7y_47695/08_2026/9e7y_47695.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.038 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 124 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 18053 2.51 5 N 5231 2.21 5 O 5903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29409 Number of models: 1 Model: "" Number of chains: 13 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: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1706 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8620 Classifications: {'peptide': 1113} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1050} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 9777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9777 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 56, 'TRANS': 1194} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 75} Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2422 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 765 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: "N" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1174 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "R" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 1} Link IDs: {'rna3p': 6} Chain: "T" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1176 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} 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 12528 SG CYS D 60 78.467 69.511 58.444 1.00193.92 S ATOM 12546 SG CYS D 62 76.826 69.121 55.212 1.00207.06 S ATOM 12655 SG CYS D 75 80.521 69.393 55.407 1.00197.42 S ATOM 12681 SG CYS D 78 78.372 72.441 56.131 1.00190.49 S ATOM 19002 SG CYS D 891 109.856 108.146 104.721 1.00152.04 S ATOM 19569 SG CYS D 968 106.450 108.567 103.003 1.00143.77 S ATOM 19611 SG CYS D 975 106.942 106.057 106.130 1.00142.51 S ATOM 19629 SG CYS D 978 107.194 109.923 106.563 1.00149.14 S Time building chain proxies: 6.68, per 1000 atoms: 0.23 Number of scatterers: 29409 At special positions: 0 Unit cell: (133.424, 172.16, 187.224, 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 95 16.00 P 124 15.00 Mg 1 11.99 O 5903 8.00 N 5231 7.00 C 18053 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 - 3.00 Amino acid : True - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " Number of angles added : 12 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6398 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 47 sheets defined 43.3% alpha, 15.4% beta 54 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.580A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.590A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.114A 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 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.721A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.030A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.543A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.653A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.526A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 292 through 302 removed outlier: 4.021A pdb=" N LYS C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 405 removed outlier: 4.167A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (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 476 through 480 removed outlier: 3.644A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 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 629 through 638 removed outlier: 4.226A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.932A 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 777 through 783 removed outlier: 4.073A pdb=" N ASP C 783 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.673A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 Processing helix chain 'C' and resid 1082 through 1092 Processing helix chain 'C' and resid 1097 through 1109 removed outlier: 3.533A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 4.065A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1123 " --> pdb=" O GLU C1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.623A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 142 through 187 Processing helix chain 'D' and resid 192 through 228 removed outlier: 4.031A pdb=" N ILE D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.967A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.535A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.974A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.515A 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 339 through 361 removed outlier: 3.819A 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 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.723A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (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 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.612A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 727 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.691A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.546A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.017A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 removed outlier: 3.559A pdb=" N ILE D 916 " --> pdb=" O ASP D 913 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU D 917 " --> pdb=" O PRO D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 917' Processing helix chain 'D' and resid 945 through 956 removed outlier: 3.530A pdb=" N ILE D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1144 removed outlier: 3.631A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.717A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.295A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.549A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1239 Processing helix chain 'D' and resid 1247 through 1255 removed outlier: 3.858A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1264 removed outlier: 3.817A pdb=" N ILE D1264 " --> pdb=" O GLY D1261 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.863A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.659A pdb=" N ALA E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 226 through 236 removed outlier: 3.590A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.019A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 309 removed outlier: 3.533A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 334 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.007A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.820A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.683A pdb=" N VAL F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F 479 " --> pdb=" O VAL F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 514 removed outlier: 3.873A pdb=" N ILE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 removed outlier: 3.581A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 50 through 57 removed outlier: 3.952A pdb=" N GLU M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR M 55 " --> pdb=" O GLU M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 removed outlier: 3.685A pdb=" N LEU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.590A pdb=" N ARG M 88 " --> pdb=" O ASN M 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 146 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.757A 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: 7.442A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.079A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.630A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 6.802A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.745A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.320A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.320A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (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 376 through 379 removed outlier: 6.554A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 212 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: 5.188A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.638A 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 541 through 542 removed outlier: 4.612A pdb=" N VAL C 561 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.694A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 687 " --> pdb=" O ASP C 704 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.830A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.905A 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: 7.726A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 748 through 759 removed outlier: 3.643A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (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 784 through 785 removed outlier: 3.682A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.710A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 906 through 907 Processing sheet with id=AD4, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.566A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD7, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.597A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD9, first strand: chain 'D' and resid 73 through 74 removed outlier: 4.086A pdb=" N ILE D 73 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.023A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.474A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE4, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.937A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE6, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.510A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 903 through 904 removed outlier: 3.767A pdb=" N ILE D 911 " --> pdb=" O GLU D 903 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1063 through 1068 removed outlier: 3.673A pdb=" N ARG D1052 " --> pdb=" O VAL D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AF1, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AF2, first strand: chain 'J' and resid 41 through 45 1267 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.31: 4901 1.31 - 1.58: 24840 1.58 - 1.84: 408 1.84 - 2.10: 0 2.10 - 2.36: 1 Bond restraints: 30150 Sorted by residual: bond pdb=" CB PRO J 70 " pdb=" CG PRO J 70 " ideal model delta sigma weight residual 1.492 2.364 -0.872 5.00e-02 4.00e+02 3.04e+02 bond pdb=" CG PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 1.503 1.052 0.451 3.40e-02 8.65e+02 1.76e+02 bond pdb=" C1' G R 6 " pdb=" N9 G R 6 " ideal model delta sigma weight residual 1.483 1.350 0.133 1.50e-02 4.44e+03 7.92e+01 bond pdb=" N PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.40e+01 bond pdb=" C1' DG T 23 " pdb=" N9 DG T 23 " ideal model delta sigma weight residual 1.468 1.375 0.093 1.40e-02 5.10e+03 4.42e+01 ... (remaining 30145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.83: 41356 9.83 - 19.66: 8 19.66 - 29.49: 3 29.49 - 39.32: 0 39.32 - 49.15: 1 Bond angle restraints: 41368 Sorted by residual: angle pdb=" CB PRO J 70 " pdb=" CG PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 106.10 56.95 49.15 3.20e+00 9.77e-02 2.36e+02 angle pdb=" N PRO J 70 " pdb=" CD PRO J 70 " pdb=" CG PRO J 70 " ideal model delta sigma weight residual 103.20 88.82 14.38 1.50e+00 4.44e-01 9.19e+01 angle pdb=" O3' DC T 17 " pdb=" P DC T 18 " pdb=" OP2 DC T 18 " ideal model delta sigma weight residual 108.00 81.28 26.72 3.00e+00 1.11e-01 7.94e+01 angle pdb=" N PRO J 70 " pdb=" CA PRO J 70 " pdb=" CB PRO J 70 " ideal model delta sigma weight residual 103.25 94.70 8.55 1.05e+00 9.07e-01 6.64e+01 angle pdb=" CA PRO J 70 " pdb=" N PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 112.00 101.32 10.68 1.40e+00 5.10e-01 5.82e+01 ... (remaining 41363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 17128 33.70 - 67.40: 970 67.40 - 101.11: 47 101.11 - 134.81: 0 134.81 - 168.51: 2 Dihedral angle restraints: 18147 sinusoidal: 8211 harmonic: 9936 Sorted by residual: dihedral pdb=" CA ASP D1070 " pdb=" C ASP D1070 " pdb=" N GLY D1071 " pdb=" CA GLY D1071 " ideal model delta harmonic sigma weight residual -180.00 -131.03 -48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA LEU J 69 " pdb=" C LEU J 69 " pdb=" N PRO J 70 " pdb=" CA PRO J 70 " ideal model delta harmonic sigma weight residual 180.00 134.15 45.85 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA GLY D 519 " pdb=" C GLY D 519 " pdb=" N LYS D 520 " pdb=" CA LYS D 520 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 4724 0.401 - 0.803: 1 0.803 - 1.204: 0 1.204 - 1.605: 0 1.605 - 2.007: 1 Chirality restraints: 4726 Sorted by residual: chirality pdb=" P DC T 18 " pdb=" OP1 DC T 18 " pdb=" OP2 DC T 18 " pdb=" O5' DC T 18 " both_signs ideal model delta sigma weight residual True 2.34 0.33 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA THR M 26 " pdb=" N THR M 26 " pdb=" C THR M 26 " pdb=" CB THR M 26 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA PRO J 70 " pdb=" N PRO J 70 " pdb=" C PRO J 70 " pdb=" CB PRO J 70 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4723 not shown) Planarity restraints: 5007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C1062 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C GLN C1062 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN C1062 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE C1063 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D1054 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ARG D1054 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG D1054 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D1055 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 300 " -0.041 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE C 300 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE C 300 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 300 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 300 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 300 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 300 " -0.028 2.00e-02 2.50e+03 ... (remaining 5004 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 303 2.54 - 3.13: 25017 3.13 - 3.72: 49272 3.72 - 4.31: 65311 4.31 - 4.90: 104997 Nonbonded interactions: 244900 Sorted by model distance: nonbonded pdb=" O PHE C 430 " pdb=" OG SER C 434 " model vdw 1.951 3.040 nonbonded pdb=" O GLY D 257 " pdb=" OG SER D 260 " model vdw 2.020 3.040 nonbonded pdb=" OD2 ASP D 539 " pdb=" O2' A R 7 " model vdw 2.039 3.040 nonbonded pdb=" OG SER D 964 " pdb=" OE1 GLU D1155 " model vdw 2.049 3.040 nonbonded pdb=" OG SER C1050 " pdb=" O THR C1053 " model vdw 2.056 3.040 ... (remaining 244895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.009 0.872 30158 Z= 0.408 Angle : 0.982 49.147 41380 Z= 0.579 Chirality : 0.060 2.007 4726 Planarity : 0.007 0.110 5007 Dihedral : 18.447 168.510 11749 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 0.52 % Allowed : 15.54 % Favored : 83.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3441 helix: 0.28 (0.13), residues: 1361 sheet: -0.89 (0.28), residues: 348 loop : -1.29 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 219 TYR 0.023 0.002 TYR C 306 PHE 0.051 0.003 PHE C 300 TRP 0.014 0.002 TRP M 112 HIS 0.014 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.40 (30150) covalent geometry : angle 0.98209 / 0.58 (41368) hydrogen bonds : bond 0.14350 / 9.83 ( 1389) hydrogen bonds : angle 6.64255 / 4.70 ( 3855) metal coordination : bond 0.09763 / 4.89 ( 8) metal coordination : angle 0.07024 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1337 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.7821 (p0) cc_final: 0.7475 (p0) REVERT: A 96 TYR cc_start: 0.8394 (m-80) cc_final: 0.7703 (m-10) REVERT: A 213 LYS cc_start: 0.8683 (tttt) cc_final: 0.8384 (tmtt) REVERT: A 219 PHE cc_start: 0.7716 (m-80) cc_final: 0.7415 (m-80) REVERT: B 39 ARG cc_start: 0.9160 (tmm-80) cc_final: 0.8719 (ttp-110) REVERT: B 42 LEU cc_start: 0.9613 (mt) cc_final: 0.9270 (mt) REVERT: B 120 ASN cc_start: 0.9058 (t0) cc_final: 0.8558 (t0) REVERT: B 125 ILE cc_start: 0.9359 (tp) cc_final: 0.9053 (tp) REVERT: B 151 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8666 (tm-30) REVERT: C 57 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 69 ARG cc_start: 0.8826 (ttp-170) cc_final: 0.7913 (ttt-90) REVERT: C 88 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 175 VAL cc_start: 0.9339 (t) cc_final: 0.9131 (p) REVERT: C 177 SER cc_start: 0.8758 (m) cc_final: 0.8439 (p) REVERT: C 235 THR cc_start: 0.8713 (p) cc_final: 0.8395 (p) REVERT: C 239 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7742 (mmtm) REVERT: C 277 ILE cc_start: 0.9463 (pt) cc_final: 0.9233 (pt) REVERT: C 278 TYR cc_start: 0.8710 (t80) cc_final: 0.8293 (t80) REVERT: C 319 LYS cc_start: 0.8423 (tptm) cc_final: 0.8039 (tttp) REVERT: C 404 MET cc_start: 0.8531 (mmm) cc_final: 0.8329 (tpp) REVERT: C 487 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8321 (tp30) REVERT: C 511 PHE cc_start: 0.8143 (m-80) cc_final: 0.7684 (m-10) REVERT: C 516 TYR cc_start: 0.7949 (m-80) cc_final: 0.7110 (m-80) REVERT: C 531 LEU cc_start: 0.8660 (mt) cc_final: 0.7840 (mt) REVERT: C 536 GLU cc_start: 0.8182 (tt0) cc_final: 0.7887 (tt0) REVERT: C 543 GLN cc_start: 0.7836 (tt0) cc_final: 0.7309 (mm-40) REVERT: C 578 TYR cc_start: 0.8161 (m-80) cc_final: 0.7886 (m-80) REVERT: C 586 MET cc_start: 0.8531 (ptm) cc_final: 0.8216 (ptm) REVERT: C 661 MET cc_start: 0.8264 (tpp) cc_final: 0.7786 (tpp) REVERT: C 750 ILE cc_start: 0.9249 (mm) cc_final: 0.8960 (mt) REVERT: C 820 LEU cc_start: 0.9423 (tp) cc_final: 0.9185 (tt) REVERT: C 846 LYS cc_start: 0.8904 (tptt) cc_final: 0.8638 (tppt) REVERT: C 867 GLU cc_start: 0.8535 (tt0) cc_final: 0.7835 (tp30) REVERT: C 873 VAL cc_start: 0.8851 (t) cc_final: 0.8587 (p) REVERT: C 884 LYS cc_start: 0.8099 (tttt) cc_final: 0.7650 (tttt) REVERT: C 926 MET cc_start: 0.8649 (tpt) cc_final: 0.8344 (tpp) REVERT: C 933 GLU cc_start: 0.8305 (tt0) cc_final: 0.7993 (tt0) REVERT: C 942 SER cc_start: 0.9018 (m) cc_final: 0.8568 (t) REVERT: C 947 ASP cc_start: 0.8134 (m-30) cc_final: 0.7476 (t0) REVERT: C 1024 THR cc_start: 0.9539 (m) cc_final: 0.9323 (p) REVERT: C 1040 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8340 (mptt) REVERT: C 1057 LEU cc_start: 0.9227 (tp) cc_final: 0.9020 (tp) REVERT: C 1070 GLU cc_start: 0.7812 (pm20) cc_final: 0.7105 (pm20) REVERT: C 1071 MET cc_start: 0.7824 (mpp) cc_final: 0.7315 (mpp) REVERT: C 1090 THR cc_start: 0.8890 (m) cc_final: 0.8613 (p) REVERT: C 1126 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9021 (mmtm) REVERT: C 1131 LEU cc_start: 0.9273 (mt) cc_final: 0.8961 (tt) REVERT: D 106 TYR cc_start: 0.8538 (m-80) cc_final: 0.7939 (m-80) REVERT: D 148 LEU cc_start: 0.9710 (tt) cc_final: 0.9410 (tp) REVERT: D 234 LEU cc_start: 0.8339 (pt) cc_final: 0.7594 (tp) REVERT: D 240 LEU cc_start: 0.9664 (mm) cc_final: 0.9446 (pp) REVERT: D 252 PHE cc_start: 0.7234 (p90) cc_final: 0.6961 (p90) REVERT: D 262 GLN cc_start: 0.9429 (tt0) cc_final: 0.9146 (tm-30) REVERT: D 399 LEU cc_start: 0.8833 (mm) cc_final: 0.8589 (mm) REVERT: D 427 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7561 (ttm-80) REVERT: D 471 SER cc_start: 0.9104 (t) cc_final: 0.7728 (t) REVERT: D 576 MET cc_start: 0.8030 (ppp) cc_final: 0.7589 (ppp) REVERT: D 581 MET cc_start: 0.8095 (mtm) cc_final: 0.7677 (mtm) REVERT: D 715 LYS cc_start: 0.9668 (mttt) cc_final: 0.9243 (mtpp) REVERT: D 765 LEU cc_start: 0.7093 (pt) cc_final: 0.6742 (mp) REVERT: D 800 ILE cc_start: 0.8717 (tp) cc_final: 0.7975 (tp) REVERT: D 838 SER cc_start: 0.6341 (m) cc_final: 0.6089 (p) REVERT: D 1139 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7321 (tm-30) REVERT: D 1235 ASP cc_start: 0.8877 (t0) cc_final: 0.8661 (m-30) REVERT: D 1238 ILE cc_start: 0.9298 (mt) cc_final: 0.9052 (mm) REVERT: D 1264 ILE cc_start: 0.8631 (pt) cc_final: 0.8364 (pt) REVERT: D 1267 TYR cc_start: 0.7853 (m-80) cc_final: 0.7179 (m-10) REVERT: E 65 ASN cc_start: 0.8828 (t0) cc_final: 0.8496 (t0) REVERT: E 66 ASP cc_start: 0.8337 (m-30) cc_final: 0.8048 (m-30) REVERT: E 67 TYR cc_start: 0.9151 (t80) cc_final: 0.8730 (t80) REVERT: E 84 GLU cc_start: 0.7975 (tp30) cc_final: 0.7681 (tp30) REVERT: E 103 LEU cc_start: 0.9169 (mt) cc_final: 0.8768 (mt) REVERT: F 263 MET cc_start: 0.8609 (mmp) cc_final: 0.8294 (mmm) REVERT: F 310 TYR cc_start: 0.7813 (m-80) cc_final: 0.7451 (m-10) REVERT: F 337 TYR cc_start: 0.7895 (p90) cc_final: 0.7468 (p90) REVERT: F 371 HIS cc_start: 0.9136 (p90) cc_final: 0.8647 (p90) REVERT: F 397 GLU cc_start: 0.9582 (pt0) cc_final: 0.9366 (pp20) REVERT: F 399 LEU cc_start: 0.9532 (mt) cc_final: 0.9222 (mm) REVERT: F 423 LEU cc_start: 0.7717 (mp) cc_final: 0.6534 (mm) REVERT: M 71 PHE cc_start: 0.9058 (m-80) cc_final: 0.8747 (m-80) outliers start: 15 outliers final: 9 residues processed: 1345 average time/residue: 0.2198 time to fit residues: 450.9016 Evaluate side-chains 934 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 925 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN B 20 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS C 479 HIS ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS C1034 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN D1145 GLN ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 100 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.112825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082109 restraints weight = 98870.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084697 restraints weight = 56017.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085425 restraints weight = 33141.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086021 restraints weight = 27287.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086425 restraints weight = 24963.302| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 30158 Z= 0.240 Angle : 0.858 24.449 41380 Z= 0.451 Chirality : 0.058 1.901 4726 Planarity : 0.009 0.367 5007 Dihedral : 17.417 177.712 5172 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 0.45 % Allowed : 5.38 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3441 helix: 0.17 (0.13), residues: 1403 sheet: -0.84 (0.26), residues: 392 loop : -1.34 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 229 TYR 0.051 0.002 TYR E 56 PHE 0.034 0.003 PHE M 3 TRP 0.021 0.003 TRP J 82 HIS 0.016 0.002 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (30150) covalent geometry : angle 0.85423 / 0.45 (41368) hydrogen bonds : bond 0.05749 / 3.86 ( 1389) hydrogen bonds : angle 5.82407 / 4.10 ( 3855) metal coordination : bond 0.01444 / 0.60 ( 8) metal coordination : angle 4.82841 / 2.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1114 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8605 (mp) cc_final: 0.8309 (mp) REVERT: A 34 LEU cc_start: 0.9409 (tp) cc_final: 0.9009 (tp) REVERT: A 38 LEU cc_start: 0.9773 (mt) cc_final: 0.9532 (mt) REVERT: A 52 THR cc_start: 0.9352 (t) cc_final: 0.9102 (p) REVERT: A 90 ASP cc_start: 0.8845 (p0) cc_final: 0.8378 (p0) REVERT: A 138 LEU cc_start: 0.9283 (mp) cc_final: 0.8892 (mp) REVERT: A 140 VAL cc_start: 0.9538 (t) cc_final: 0.8667 (m) REVERT: A 141 GLU cc_start: 0.8210 (tp30) cc_final: 0.7369 (mm-30) REVERT: A 208 LEU cc_start: 0.9510 (mm) cc_final: 0.9278 (mm) REVERT: B 14 LEU cc_start: 0.9064 (mt) cc_final: 0.8772 (mt) REVERT: B 20 GLN cc_start: 0.8843 (mp10) cc_final: 0.8385 (mp10) REVERT: B 39 ARG cc_start: 0.9245 (tmm-80) cc_final: 0.8275 (ttp80) REVERT: B 40 ARG cc_start: 0.8871 (mmp-170) cc_final: 0.8330 (mmm160) REVERT: B 95 MET cc_start: 0.8265 (ttt) cc_final: 0.8001 (ttt) REVERT: B 120 ASN cc_start: 0.9397 (t0) cc_final: 0.8930 (t0) REVERT: B 151 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8634 (tm-30) REVERT: B 165 ASP cc_start: 0.9155 (m-30) cc_final: 0.8697 (m-30) REVERT: B 188 ASP cc_start: 0.9452 (t70) cc_final: 0.9243 (t0) REVERT: B 213 LYS cc_start: 0.9525 (tptp) cc_final: 0.9313 (tppt) REVERT: C 57 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8873 (mm-40) REVERT: C 59 ASP cc_start: 0.9515 (m-30) cc_final: 0.9252 (m-30) REVERT: C 87 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8731 (mp0) REVERT: C 89 VAL cc_start: 0.9818 (t) cc_final: 0.9609 (t) REVERT: C 93 LEU cc_start: 0.9222 (tp) cc_final: 0.8904 (tp) REVERT: C 102 SER cc_start: 0.8879 (m) cc_final: 0.8300 (p) REVERT: C 127 MET cc_start: 0.8909 (tmm) cc_final: 0.8185 (tmm) REVERT: C 199 LEU cc_start: 0.9359 (pp) cc_final: 0.9059 (mt) REVERT: C 202 VAL cc_start: 0.9421 (p) cc_final: 0.9109 (p) REVERT: C 252 PHE cc_start: 0.8983 (m-80) cc_final: 0.8704 (m-80) REVERT: C 264 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8827 (ptpp) REVERT: C 268 VAL cc_start: 0.9074 (m) cc_final: 0.8786 (p) REVERT: C 275 LEU cc_start: 0.9580 (tt) cc_final: 0.9289 (mt) REVERT: C 390 ARG cc_start: 0.9142 (ttm110) cc_final: 0.8822 (mtm-85) REVERT: C 393 MET cc_start: 0.9587 (mmm) cc_final: 0.9362 (mmm) REVERT: C 428 LYS cc_start: 0.9490 (ptpp) cc_final: 0.9276 (ptpp) REVERT: C 439 PHE cc_start: 0.9189 (t80) cc_final: 0.8570 (t80) REVERT: C 441 ASP cc_start: 0.8218 (m-30) cc_final: 0.7901 (m-30) REVERT: C 442 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8294 (tp-100) REVERT: C 511 PHE cc_start: 0.8483 (m-80) cc_final: 0.7599 (m-10) REVERT: C 516 TYR cc_start: 0.8510 (m-80) cc_final: 0.7353 (m-80) REVERT: C 531 LEU cc_start: 0.8666 (mt) cc_final: 0.7953 (mt) REVERT: C 536 GLU cc_start: 0.8754 (pt0) cc_final: 0.8427 (pt0) REVERT: C 543 GLN cc_start: 0.8307 (tt0) cc_final: 0.7700 (tt0) REVERT: C 585 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8225 (tp-100) REVERT: C 601 ASP cc_start: 0.9245 (t0) cc_final: 0.8615 (p0) REVERT: C 620 ARG cc_start: 0.9310 (tpm170) cc_final: 0.9039 (tpm170) REVERT: C 680 HIS cc_start: 0.7769 (m-70) cc_final: 0.7548 (m-70) REVERT: C 713 MET cc_start: 0.9009 (tpp) cc_final: 0.8483 (ptp) REVERT: C 749 SER cc_start: 0.9570 (m) cc_final: 0.9061 (p) REVERT: C 818 GLU cc_start: 0.9590 (tp30) cc_final: 0.9337 (tm-30) REVERT: C 839 VAL cc_start: 0.8944 (t) cc_final: 0.8559 (t) REVERT: C 846 LYS cc_start: 0.9231 (tptt) cc_final: 0.8927 (tppt) REVERT: C 850 ILE cc_start: 0.8655 (mp) cc_final: 0.8363 (mm) REVERT: C 873 VAL cc_start: 0.9109 (t) cc_final: 0.8456 (p) REVERT: C 892 LYS cc_start: 0.9119 (ptpt) cc_final: 0.8663 (ptpt) REVERT: C 904 MET cc_start: 0.9094 (tpp) cc_final: 0.8158 (tpp) REVERT: C 909 ASP cc_start: 0.8138 (p0) cc_final: 0.7924 (p0) REVERT: C 926 MET cc_start: 0.8919 (tpt) cc_final: 0.8268 (tpp) REVERT: C 933 GLU cc_start: 0.8640 (tt0) cc_final: 0.8204 (tt0) REVERT: C 942 SER cc_start: 0.8948 (m) cc_final: 0.8680 (t) REVERT: C 947 ASP cc_start: 0.9027 (m-30) cc_final: 0.8079 (t0) REVERT: C 985 LEU cc_start: 0.9526 (mm) cc_final: 0.9324 (mm) REVERT: C 1001 LEU cc_start: 0.9147 (mt) cc_final: 0.8718 (mt) REVERT: C 1031 MET cc_start: 0.8671 (mtm) cc_final: 0.7922 (mtm) REVERT: C 1033 LEU cc_start: 0.9423 (mp) cc_final: 0.9209 (mp) REVERT: C 1034 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8775 (t-90) REVERT: C 1039 ASP cc_start: 0.9228 (m-30) cc_final: 0.9024 (m-30) REVERT: C 1040 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7957 (mptt) REVERT: C 1070 GLU cc_start: 0.8703 (pm20) cc_final: 0.8133 (pm20) REVERT: C 1071 MET cc_start: 0.8342 (mpp) cc_final: 0.7584 (mpp) REVERT: C 1076 MET cc_start: 0.8981 (ttm) cc_final: 0.8601 (ttm) REVERT: C 1090 THR cc_start: 0.8871 (m) cc_final: 0.8615 (p) REVERT: C 1128 LEU cc_start: 0.9661 (mt) cc_final: 0.9267 (mt) REVERT: C 1133 LEU cc_start: 0.9384 (mt) cc_final: 0.9120 (mt) REVERT: D 29 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8849 (ptpp) REVERT: D 33 THR cc_start: 0.8665 (p) cc_final: 0.8316 (p) REVERT: D 52 PHE cc_start: 0.7511 (m-80) cc_final: 0.6679 (m-10) REVERT: D 92 MET cc_start: 0.7643 (mmm) cc_final: 0.7263 (tpt) REVERT: D 113 ARG cc_start: 0.9288 (mpt180) cc_final: 0.9014 (mmt90) REVERT: D 118 LEU cc_start: 0.9300 (mm) cc_final: 0.8886 (mm) REVERT: D 119 ASP cc_start: 0.8561 (t70) cc_final: 0.8293 (t0) REVERT: D 120 LEU cc_start: 0.8867 (mm) cc_final: 0.8315 (tp) REVERT: D 252 PHE cc_start: 0.8079 (p90) cc_final: 0.7653 (p90) REVERT: D 262 GLN cc_start: 0.9654 (tt0) cc_final: 0.9069 (tm-30) REVERT: D 263 LYS cc_start: 0.9440 (tppt) cc_final: 0.9200 (mtmm) REVERT: D 341 ASN cc_start: 0.8960 (m-40) cc_final: 0.8640 (m-40) REVERT: D 382 PHE cc_start: 0.9100 (m-80) cc_final: 0.8783 (m-80) REVERT: D 397 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8402 (tmm-80) REVERT: D 407 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7903 (mmtt) REVERT: D 427 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.7749 (ttm-80) REVERT: D 438 LEU cc_start: 0.9188 (tp) cc_final: 0.8949 (tp) REVERT: D 471 SER cc_start: 0.9327 (t) cc_final: 0.8658 (p) REVERT: D 475 MET cc_start: 0.9003 (mmp) cc_final: 0.8648 (mmp) REVERT: D 478 ARG cc_start: 0.9295 (tmt170) cc_final: 0.8859 (ttp80) REVERT: D 500 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8823 (tmm-80) REVERT: D 515 MET cc_start: 0.8428 (mmp) cc_final: 0.8075 (mmm) REVERT: D 527 LEU cc_start: 0.9405 (mt) cc_final: 0.9114 (mt) REVERT: D 563 ASN cc_start: 0.8940 (m-40) cc_final: 0.8644 (m-40) REVERT: D 576 MET cc_start: 0.8929 (ppp) cc_final: 0.8623 (ppp) REVERT: D 581 MET cc_start: 0.8699 (mtm) cc_final: 0.8123 (mtm) REVERT: D 636 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8567 (tpp80) REVERT: D 676 LEU cc_start: 0.9597 (mp) cc_final: 0.9384 (mp) REVERT: D 706 MET cc_start: 0.8616 (ptm) cc_final: 0.8361 (pmm) REVERT: D 707 ILE cc_start: 0.9453 (tt) cc_final: 0.9217 (tt) REVERT: D 715 LYS cc_start: 0.9693 (mttt) cc_final: 0.9357 (mtpp) REVERT: D 717 LYS cc_start: 0.9220 (tmmt) cc_final: 0.8609 (ttpp) REVERT: D 757 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8968 (tm-30) REVERT: D 780 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8848 (mm-30) REVERT: D 784 GLU cc_start: 0.9268 (mm-30) cc_final: 0.9042 (mm-30) REVERT: D 800 ILE cc_start: 0.9342 (tp) cc_final: 0.9081 (tp) REVERT: D 804 ASP cc_start: 0.8652 (m-30) cc_final: 0.8433 (p0) REVERT: D 815 ARG cc_start: 0.9462 (tmm-80) cc_final: 0.9189 (ptm-80) REVERT: D 838 SER cc_start: 0.7526 (m) cc_final: 0.6829 (p) REVERT: D 862 ASP cc_start: 0.8973 (t0) cc_final: 0.8627 (t0) REVERT: D 866 ARG cc_start: 0.9183 (ptt180) cc_final: 0.8587 (ptt-90) REVERT: D 916 ILE cc_start: 0.9275 (tp) cc_final: 0.8993 (mm) REVERT: D 990 ASP cc_start: 0.8239 (m-30) cc_final: 0.7837 (m-30) REVERT: D 993 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8242 (mm-30) REVERT: D 1032 GLN cc_start: 0.9413 (tm-30) cc_final: 0.8999 (tm-30) REVERT: D 1036 GLU cc_start: 0.8299 (tp30) cc_final: 0.7438 (tt0) REVERT: D 1120 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8191 (tm-30) REVERT: D 1133 HIS cc_start: 0.9186 (t70) cc_final: 0.8962 (t70) REVERT: D 1139 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8930 (tp-100) REVERT: D 1183 ARG cc_start: 0.9293 (ptp-110) cc_final: 0.8796 (ptp-170) REVERT: D 1208 MET cc_start: 0.8554 (mpp) cc_final: 0.8216 (mpp) REVERT: D 1210 ILE cc_start: 0.9035 (pt) cc_final: 0.8833 (pt) REVERT: E 59 LYS cc_start: 0.9134 (mttt) cc_final: 0.8927 (mtpp) REVERT: E 66 ASP cc_start: 0.8662 (m-30) cc_final: 0.8279 (m-30) REVERT: E 79 VAL cc_start: 0.9066 (t) cc_final: 0.8663 (m) REVERT: E 103 LEU cc_start: 0.9116 (mt) cc_final: 0.8828 (mt) REVERT: F 252 ARG cc_start: 0.9245 (mtp85) cc_final: 0.8743 (mmm160) REVERT: F 263 MET cc_start: 0.8711 (mmp) cc_final: 0.8490 (mmm) REVERT: F 310 TYR cc_start: 0.8480 (m-80) cc_final: 0.7699 (m-10) REVERT: F 323 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9030 (mm-30) REVERT: F 333 GLU cc_start: 0.8110 (tt0) cc_final: 0.7096 (tm-30) REVERT: F 334 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7795 (mmmt) REVERT: F 348 THR cc_start: 0.9050 (m) cc_final: 0.8849 (m) REVERT: F 372 MET cc_start: 0.9617 (mmp) cc_final: 0.9336 (mmm) REVERT: F 397 GLU cc_start: 0.9582 (pt0) cc_final: 0.9377 (pp20) REVERT: F 412 GLU cc_start: 0.9714 (tp30) cc_final: 0.9270 (tp30) REVERT: F 415 GLN cc_start: 0.9724 (tm-30) cc_final: 0.9450 (tm-30) REVERT: F 482 THR cc_start: 0.8582 (m) cc_final: 0.8300 (p) REVERT: F 483 ASP cc_start: 0.7956 (t0) cc_final: 0.7675 (t70) REVERT: F 525 ASP cc_start: 0.9145 (m-30) cc_final: 0.8536 (p0) REVERT: J 32 TYR cc_start: 0.8644 (m-80) cc_final: 0.8242 (m-80) REVERT: J 86 LEU cc_start: 0.9664 (tp) cc_final: 0.9384 (mt) REVERT: M 156 GLU cc_start: 0.9667 (tm-30) cc_final: 0.9407 (mm-30) outliers start: 13 outliers final: 4 residues processed: 1122 average time/residue: 0.2138 time to fit residues: 369.0735 Evaluate side-chains 850 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 845 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 208 optimal weight: 0.1980 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 289 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081877 restraints weight = 97467.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084014 restraints weight = 56918.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084677 restraints weight = 33013.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086147 restraints weight = 27234.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086245 restraints weight = 21818.986| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30158 Z= 0.185 Angle : 0.800 24.426 41380 Z= 0.418 Chirality : 0.056 1.915 4726 Planarity : 0.008 0.373 5007 Dihedral : 17.489 177.860 5172 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3441 helix: 0.20 (0.13), residues: 1406 sheet: -0.81 (0.26), residues: 397 loop : -1.29 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 500 TYR 0.037 0.002 TYR F 346 PHE 0.032 0.002 PHE B 30 TRP 0.018 0.002 TRP M 112 HIS 0.012 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (30150) covalent geometry : angle 0.79843 / 0.42 (41368) hydrogen bonds : bond 0.05170 / 3.51 ( 1389) hydrogen bonds : angle 5.52040 / 3.89 ( 3855) metal coordination : bond 0.00883 / 0.36 ( 8) metal coordination : angle 3.44951 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1045 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 27 GLU cc_start: 0.8872 (tp30) cc_final: 0.8475 (tp30) REVERT: A 30 PHE cc_start: 0.7715 (m-10) cc_final: 0.7387 (m-80) REVERT: A 138 LEU cc_start: 0.9369 (mp) cc_final: 0.8964 (mp) REVERT: A 141 GLU cc_start: 0.8289 (tp30) cc_final: 0.7846 (tp30) REVERT: A 165 ASP cc_start: 0.8867 (m-30) cc_final: 0.8558 (m-30) REVERT: A 208 LEU cc_start: 0.9533 (mm) cc_final: 0.9289 (mm) REVERT: A 219 PHE cc_start: 0.8082 (m-80) cc_final: 0.7779 (m-80) REVERT: B 14 LEU cc_start: 0.9099 (mt) cc_final: 0.8548 (mt) REVERT: B 18 ARG cc_start: 0.9141 (ptt90) cc_final: 0.8832 (ptt90) REVERT: B 20 GLN cc_start: 0.8757 (mp10) cc_final: 0.8213 (mp10) REVERT: B 39 ARG cc_start: 0.9279 (tmm-80) cc_final: 0.8677 (ttp80) REVERT: B 40 ARG cc_start: 0.8904 (mmp-170) cc_final: 0.8422 (mmm160) REVERT: B 42 LEU cc_start: 0.9793 (mt) cc_final: 0.9577 (mt) REVERT: B 120 ASN cc_start: 0.9394 (t0) cc_final: 0.8943 (t0) REVERT: B 151 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8616 (tm-30) REVERT: B 165 ASP cc_start: 0.8880 (m-30) cc_final: 0.8598 (m-30) REVERT: B 173 LYS cc_start: 0.9074 (tptp) cc_final: 0.8865 (tptt) REVERT: B 188 ASP cc_start: 0.9519 (t70) cc_final: 0.9277 (t0) REVERT: B 219 PHE cc_start: 0.9284 (m-80) cc_final: 0.9006 (m-80) REVERT: C 48 LEU cc_start: 0.9075 (mm) cc_final: 0.8803 (mm) REVERT: C 87 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8961 (mp0) REVERT: C 102 SER cc_start: 0.8738 (m) cc_final: 0.8212 (p) REVERT: C 199 LEU cc_start: 0.9312 (pp) cc_final: 0.9006 (mt) REVERT: C 202 VAL cc_start: 0.9264 (p) cc_final: 0.9003 (p) REVERT: C 230 ARG cc_start: 0.8047 (ptt180) cc_final: 0.7790 (ptt90) REVERT: C 254 PHE cc_start: 0.6672 (p90) cc_final: 0.6290 (p90) REVERT: C 264 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8814 (ptpp) REVERT: C 275 LEU cc_start: 0.9437 (tt) cc_final: 0.9163 (mt) REVERT: C 350 GLU cc_start: 0.7991 (pt0) cc_final: 0.7738 (pt0) REVERT: C 390 ARG cc_start: 0.9246 (ttm110) cc_final: 0.8887 (ttm110) REVERT: C 439 PHE cc_start: 0.9173 (t80) cc_final: 0.8954 (t80) REVERT: C 483 MET cc_start: 0.8353 (tpt) cc_final: 0.8128 (tpt) REVERT: C 511 PHE cc_start: 0.8484 (m-80) cc_final: 0.7473 (m-10) REVERT: C 516 TYR cc_start: 0.8562 (m-80) cc_final: 0.7937 (m-80) REVERT: C 531 LEU cc_start: 0.8630 (mt) cc_final: 0.8114 (mt) REVERT: C 543 GLN cc_start: 0.8191 (tt0) cc_final: 0.7568 (tt0) REVERT: C 585 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8070 (tp-100) REVERT: C 593 MET cc_start: 0.8858 (mmm) cc_final: 0.8626 (mmm) REVERT: C 601 ASP cc_start: 0.9167 (t0) cc_final: 0.8635 (p0) REVERT: C 604 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8000 (tpp-160) REVERT: C 611 MET cc_start: 0.8481 (ptp) cc_final: 0.8247 (ptt) REVERT: C 622 GLU cc_start: 0.8042 (pt0) cc_final: 0.7633 (pt0) REVERT: C 625 LEU cc_start: 0.9205 (mm) cc_final: 0.8862 (mm) REVERT: C 651 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 713 MET cc_start: 0.8922 (tpp) cc_final: 0.8585 (ptt) REVERT: C 732 GLU cc_start: 0.8490 (tp30) cc_final: 0.8216 (tp30) REVERT: C 741 LEU cc_start: 0.9482 (mt) cc_final: 0.9220 (mt) REVERT: C 749 SER cc_start: 0.9526 (m) cc_final: 0.8952 (p) REVERT: C 814 LEU cc_start: 0.9002 (mm) cc_final: 0.8676 (mm) REVERT: C 815 THR cc_start: 0.9225 (p) cc_final: 0.9002 (p) REVERT: C 818 GLU cc_start: 0.9572 (tp30) cc_final: 0.9331 (tm-30) REVERT: C 819 ARG cc_start: 0.9492 (mtt90) cc_final: 0.9255 (mtt-85) REVERT: C 846 LYS cc_start: 0.9284 (tptt) cc_final: 0.8934 (tppt) REVERT: C 867 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8270 (mp0) REVERT: C 873 VAL cc_start: 0.9003 (t) cc_final: 0.8473 (p) REVERT: C 892 LYS cc_start: 0.9162 (ptpt) cc_final: 0.8580 (ptpt) REVERT: C 933 GLU cc_start: 0.8801 (tt0) cc_final: 0.8145 (tt0) REVERT: C 944 TRP cc_start: 0.8632 (p90) cc_final: 0.8150 (p90) REVERT: C 947 ASP cc_start: 0.9039 (m-30) cc_final: 0.8059 (t0) REVERT: C 985 LEU cc_start: 0.9622 (mm) cc_final: 0.9345 (mm) REVERT: C 1031 MET cc_start: 0.8791 (mtm) cc_final: 0.8024 (mtm) REVERT: C 1040 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7764 (mptt) REVERT: C 1077 GLN cc_start: 0.9396 (mt0) cc_final: 0.9097 (mp10) REVERT: C 1090 THR cc_start: 0.8971 (m) cc_final: 0.8705 (p) REVERT: C 1091 ILE cc_start: 0.8869 (pt) cc_final: 0.8652 (pt) REVERT: C 1127 GLU cc_start: 0.9073 (pp20) cc_final: 0.8780 (pp20) REVERT: C 1128 LEU cc_start: 0.9507 (mt) cc_final: 0.9217 (mt) REVERT: C 1131 LEU cc_start: 0.9592 (mt) cc_final: 0.9363 (mt) REVERT: C 1138 LEU cc_start: 0.7990 (tp) cc_final: 0.7747 (tp) REVERT: D 29 LYS cc_start: 0.9157 (ptpp) cc_final: 0.8954 (ptpp) REVERT: D 52 PHE cc_start: 0.7732 (m-80) cc_final: 0.7046 (m-10) REVERT: D 66 LYS cc_start: 0.9172 (ptpp) cc_final: 0.8907 (mmmt) REVERT: D 92 MET cc_start: 0.8161 (mmm) cc_final: 0.7575 (tpt) REVERT: D 118 LEU cc_start: 0.9334 (mm) cc_final: 0.8853 (mm) REVERT: D 119 ASP cc_start: 0.8475 (t70) cc_final: 0.8192 (t0) REVERT: D 120 LEU cc_start: 0.8853 (mm) cc_final: 0.8398 (tp) REVERT: D 205 MET cc_start: 0.8406 (mmm) cc_final: 0.7770 (mmm) REVERT: D 215 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8641 (tm-30) REVERT: D 252 PHE cc_start: 0.8032 (p90) cc_final: 0.7687 (p90) REVERT: D 256 MET cc_start: 0.7441 (tpp) cc_final: 0.6943 (tpp) REVERT: D 262 GLN cc_start: 0.9509 (tt0) cc_final: 0.8994 (tm-30) REVERT: D 302 PHE cc_start: 0.9166 (m-80) cc_final: 0.8701 (m-10) REVERT: D 341 ASN cc_start: 0.8808 (m-40) cc_final: 0.8513 (m-40) REVERT: D 345 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8468 (ttt180) REVERT: D 346 ARG cc_start: 0.9118 (ttm110) cc_final: 0.8225 (ptp-110) REVERT: D 382 PHE cc_start: 0.9003 (m-80) cc_final: 0.8747 (m-80) REVERT: D 427 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7662 (ttm-80) REVERT: D 471 SER cc_start: 0.9204 (t) cc_final: 0.8724 (p) REVERT: D 475 MET cc_start: 0.8913 (mmp) cc_final: 0.8616 (mmp) REVERT: D 505 HIS cc_start: 0.9202 (p-80) cc_final: 0.8981 (p90) REVERT: D 506 ARG cc_start: 0.9307 (ttt180) cc_final: 0.9085 (ttt180) REVERT: D 515 MET cc_start: 0.8304 (mmp) cc_final: 0.8030 (mmm) REVERT: D 523 GLN cc_start: 0.8733 (tt0) cc_final: 0.8274 (tp40) REVERT: D 560 LEU cc_start: 0.9559 (tp) cc_final: 0.9334 (tp) REVERT: D 563 ASN cc_start: 0.8812 (m-40) cc_final: 0.8592 (m-40) REVERT: D 574 LEU cc_start: 0.9125 (mt) cc_final: 0.8918 (mt) REVERT: D 576 MET cc_start: 0.9109 (ppp) cc_final: 0.8805 (ppp) REVERT: D 581 MET cc_start: 0.8773 (mtm) cc_final: 0.8569 (mtm) REVERT: D 617 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: D 675 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8996 (tm-30) REVERT: D 706 MET cc_start: 0.8494 (ptm) cc_final: 0.8283 (pmm) REVERT: D 715 LYS cc_start: 0.9702 (mttt) cc_final: 0.9350 (mtpt) REVERT: D 717 LYS cc_start: 0.9245 (tmmt) cc_final: 0.8923 (pttp) REVERT: D 757 GLU cc_start: 0.9212 (tm-30) cc_final: 0.9009 (tm-30) REVERT: D 780 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8818 (mm-30) REVERT: D 784 GLU cc_start: 0.9230 (mm-30) cc_final: 0.9000 (mm-30) REVERT: D 800 ILE cc_start: 0.9362 (tp) cc_final: 0.8957 (tp) REVERT: D 804 ASP cc_start: 0.8638 (m-30) cc_final: 0.8241 (m-30) REVERT: D 840 PHE cc_start: 0.9037 (m-80) cc_final: 0.8602 (m-80) REVERT: D 844 LEU cc_start: 0.8601 (mm) cc_final: 0.7488 (tp) REVERT: D 866 ARG cc_start: 0.9206 (ptt180) cc_final: 0.8983 (ptt-90) REVERT: D 928 ASP cc_start: 0.8762 (p0) cc_final: 0.8450 (p0) REVERT: D 990 ASP cc_start: 0.8128 (m-30) cc_final: 0.7662 (m-30) REVERT: D 993 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8262 (mm-30) REVERT: D 1028 LEU cc_start: 0.9663 (tp) cc_final: 0.9443 (tp) REVERT: D 1036 GLU cc_start: 0.8394 (tp30) cc_final: 0.8020 (tp30) REVERT: D 1139 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8984 (tp-100) REVERT: D 1151 ASP cc_start: 0.8298 (t0) cc_final: 0.7927 (t0) REVERT: D 1231 ARG cc_start: 0.9361 (ptt180) cc_final: 0.8974 (ptt90) REVERT: D 1238 ILE cc_start: 0.9265 (mt) cc_final: 0.8979 (tp) REVERT: E 43 LEU cc_start: 0.9715 (mm) cc_final: 0.9490 (mm) REVERT: E 65 ASN cc_start: 0.9283 (t0) cc_final: 0.8913 (t0) REVERT: E 66 ASP cc_start: 0.8748 (m-30) cc_final: 0.8241 (m-30) REVERT: E 78 TYR cc_start: 0.8491 (m-10) cc_final: 0.8113 (m-10) REVERT: E 79 VAL cc_start: 0.9101 (t) cc_final: 0.8703 (m) REVERT: E 103 LEU cc_start: 0.9230 (mt) cc_final: 0.8949 (mt) REVERT: F 213 ARG cc_start: 0.8799 (ptt90) cc_final: 0.8598 (ttp80) REVERT: F 252 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8599 (mmm160) REVERT: F 258 TYR cc_start: 0.9146 (t80) cc_final: 0.8930 (t80) REVERT: F 282 MET cc_start: 0.9268 (mpp) cc_final: 0.8974 (ptp) REVERT: F 308 LYS cc_start: 0.9458 (pttp) cc_final: 0.9223 (mmmt) REVERT: F 310 TYR cc_start: 0.8709 (m-80) cc_final: 0.8198 (m-10) REVERT: F 334 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7713 (mmmt) REVERT: F 349 TRP cc_start: 0.8177 (m-10) cc_final: 0.7883 (m-10) REVERT: F 352 ARG cc_start: 0.8824 (mtp-110) cc_final: 0.8485 (mtm180) REVERT: F 372 MET cc_start: 0.9600 (mmp) cc_final: 0.9330 (mmm) REVERT: F 525 ASP cc_start: 0.9151 (m-30) cc_final: 0.8576 (p0) REVERT: J 55 LEU cc_start: 0.9253 (tp) cc_final: 0.8977 (tp) REVERT: J 86 LEU cc_start: 0.9646 (tp) cc_final: 0.9343 (mt) REVERT: J 91 ILE cc_start: 0.8920 (pt) cc_final: 0.8560 (pt) REVERT: M 71 PHE cc_start: 0.8981 (m-80) cc_final: 0.8753 (m-80) REVERT: M 156 GLU cc_start: 0.9693 (tm-30) cc_final: 0.9415 (mm-30) outliers start: 6 outliers final: 0 residues processed: 1050 average time/residue: 0.1943 time to fit residues: 317.2703 Evaluate side-chains 824 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 823 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 229 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 316 optimal weight: 9.9990 chunk 344 optimal weight: 50.0000 chunk 6 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS C 889 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.079768 restraints weight = 99268.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080078 restraints weight = 55841.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080853 restraints weight = 36988.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083191 restraints weight = 30465.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083030 restraints weight = 22429.440| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30158 Z= 0.237 Angle : 0.827 24.747 41380 Z= 0.426 Chirality : 0.056 1.902 4726 Planarity : 0.008 0.359 5007 Dihedral : 17.554 177.589 5172 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3441 helix: 0.15 (0.13), residues: 1408 sheet: -0.98 (0.25), residues: 410 loop : -1.30 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 636 TYR 0.031 0.002 TYR F 526 PHE 0.026 0.002 PHE D 760 TRP 0.049 0.003 TRP M 112 HIS 0.013 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (30150) covalent geometry : angle 0.81124 / 0.43 (41368) hydrogen bonds : bond 0.05089 / 3.45 ( 1389) hydrogen bonds : angle 5.52048 / 3.88 ( 3855) metal coordination : bond 0.01217 / 0.57 ( 8) metal coordination : angle 9.42176 / 6.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 955 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8877 (tp30) cc_final: 0.8524 (tp30) REVERT: A 138 LEU cc_start: 0.9377 (mp) cc_final: 0.9005 (mp) REVERT: A 208 LEU cc_start: 0.9585 (mm) cc_final: 0.9333 (mm) REVERT: A 219 PHE cc_start: 0.8171 (m-80) cc_final: 0.7702 (m-80) REVERT: B 12 ASP cc_start: 0.9244 (t70) cc_final: 0.8952 (t0) REVERT: B 20 GLN cc_start: 0.8760 (mp10) cc_final: 0.8091 (mp10) REVERT: B 42 LEU cc_start: 0.9800 (mt) cc_final: 0.9581 (mt) REVERT: B 120 ASN cc_start: 0.9411 (t0) cc_final: 0.8934 (t0) REVERT: B 131 LYS cc_start: 0.9573 (pttm) cc_final: 0.9151 (tppt) REVERT: B 133 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8749 (mmmm) REVERT: B 151 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8620 (tm-30) REVERT: B 165 ASP cc_start: 0.9032 (m-30) cc_final: 0.8747 (m-30) REVERT: B 177 LYS cc_start: 0.8478 (mppt) cc_final: 0.8203 (mmtm) REVERT: B 219 PHE cc_start: 0.9320 (m-80) cc_final: 0.9006 (m-80) REVERT: C 87 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9204 (mt-10) REVERT: C 91 TYR cc_start: 0.9269 (t80) cc_final: 0.9037 (t80) REVERT: C 92 GLU cc_start: 0.9016 (pt0) cc_final: 0.8497 (pt0) REVERT: C 102 SER cc_start: 0.8836 (m) cc_final: 0.8404 (p) REVERT: C 127 MET cc_start: 0.8811 (tmm) cc_final: 0.8319 (tmm) REVERT: C 160 MET cc_start: 0.6858 (tpp) cc_final: 0.6485 (tpp) REVERT: C 177 SER cc_start: 0.9086 (m) cc_final: 0.8796 (t) REVERT: C 275 LEU cc_start: 0.9455 (tt) cc_final: 0.9183 (mt) REVERT: C 350 GLU cc_start: 0.8243 (pt0) cc_final: 0.7969 (pt0) REVERT: C 439 PHE cc_start: 0.9249 (t80) cc_final: 0.9032 (t80) REVERT: C 442 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8721 (tp-100) REVERT: C 466 GLU cc_start: 0.9412 (pm20) cc_final: 0.9202 (pm20) REVERT: C 482 ARG cc_start: 0.9044 (mtt90) cc_final: 0.8157 (mpt180) REVERT: C 483 MET cc_start: 0.8471 (tpt) cc_final: 0.8164 (tpp) REVERT: C 511 PHE cc_start: 0.8813 (m-80) cc_final: 0.8037 (m-10) REVERT: C 543 GLN cc_start: 0.8248 (tt0) cc_final: 0.7678 (tt0) REVERT: C 579 MET cc_start: 0.8869 (ppp) cc_final: 0.8279 (tmm) REVERT: C 601 ASP cc_start: 0.9190 (t0) cc_final: 0.8754 (p0) REVERT: C 620 ARG cc_start: 0.9270 (tpm170) cc_final: 0.8837 (tpm170) REVERT: C 672 MET cc_start: 0.7046 (ppp) cc_final: 0.6628 (ppp) REVERT: C 713 MET cc_start: 0.8830 (tpp) cc_final: 0.8441 (ptp) REVERT: C 773 ILE cc_start: 0.6868 (mm) cc_final: 0.6658 (mm) REVERT: C 818 GLU cc_start: 0.9597 (tp30) cc_final: 0.9322 (tm-30) REVERT: C 846 LYS cc_start: 0.9168 (tptt) cc_final: 0.8702 (tppt) REVERT: C 873 VAL cc_start: 0.9203 (t) cc_final: 0.8743 (p) REVERT: C 892 LYS cc_start: 0.9167 (ptpt) cc_final: 0.8753 (ptpt) REVERT: C 926 MET cc_start: 0.9089 (tpt) cc_final: 0.8436 (tpt) REVERT: C 933 GLU cc_start: 0.8474 (tt0) cc_final: 0.7994 (tt0) REVERT: C 944 TRP cc_start: 0.8653 (p90) cc_final: 0.8211 (p90) REVERT: C 947 ASP cc_start: 0.9094 (m-30) cc_final: 0.8098 (t0) REVERT: C 962 GLU cc_start: 0.8466 (mp0) cc_final: 0.8263 (mp0) REVERT: C 1002 VAL cc_start: 0.9218 (t) cc_final: 0.8996 (p) REVERT: C 1040 LYS cc_start: 0.8509 (mmtt) cc_final: 0.7972 (mptt) REVERT: C 1090 THR cc_start: 0.8900 (m) cc_final: 0.8683 (p) REVERT: C 1127 GLU cc_start: 0.9080 (pp20) cc_final: 0.8827 (pp20) REVERT: C 1128 LEU cc_start: 0.9462 (mt) cc_final: 0.9191 (mt) REVERT: D 29 LYS cc_start: 0.9193 (ptpp) cc_final: 0.8936 (ptpp) REVERT: D 52 PHE cc_start: 0.7990 (m-80) cc_final: 0.7344 (m-10) REVERT: D 66 LYS cc_start: 0.9237 (ptpp) cc_final: 0.8942 (mmmt) REVERT: D 92 MET cc_start: 0.8293 (mmm) cc_final: 0.8023 (mmm) REVERT: D 105 TRP cc_start: 0.9028 (m100) cc_final: 0.8326 (m100) REVERT: D 118 LEU cc_start: 0.9381 (mm) cc_final: 0.8930 (mm) REVERT: D 119 ASP cc_start: 0.8539 (t70) cc_final: 0.8252 (t0) REVERT: D 120 LEU cc_start: 0.8888 (mm) cc_final: 0.8451 (tp) REVERT: D 205 MET cc_start: 0.8856 (mmm) cc_final: 0.8449 (mmm) REVERT: D 252 PHE cc_start: 0.8234 (p90) cc_final: 0.7990 (p90) REVERT: D 262 GLN cc_start: 0.9519 (tt0) cc_final: 0.8998 (tm-30) REVERT: D 341 ASN cc_start: 0.8844 (m-40) cc_final: 0.8543 (m-40) REVERT: D 345 ARG cc_start: 0.8765 (ttt-90) cc_final: 0.8509 (ttt180) REVERT: D 346 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8355 (ptp-110) REVERT: D 356 ARG cc_start: 0.9405 (mtm-85) cc_final: 0.8999 (ptt-90) REVERT: D 397 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8495 (tmm-80) REVERT: D 427 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: D 471 SER cc_start: 0.9252 (t) cc_final: 0.8648 (p) REVERT: D 475 MET cc_start: 0.8973 (mmp) cc_final: 0.8680 (mmp) REVERT: D 510 GLN cc_start: 0.8111 (mp10) cc_final: 0.7699 (mp10) REVERT: D 515 MET cc_start: 0.8502 (mmp) cc_final: 0.8230 (mmm) REVERT: D 527 LEU cc_start: 0.9390 (mt) cc_final: 0.9077 (mt) REVERT: D 532 PHE cc_start: 0.8083 (m-10) cc_final: 0.7513 (m-80) REVERT: D 552 GLN cc_start: 0.8458 (mp10) cc_final: 0.8146 (mp10) REVERT: D 554 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8473 (mt-10) REVERT: D 560 LEU cc_start: 0.9576 (tp) cc_final: 0.9367 (tp) REVERT: D 563 ASN cc_start: 0.8906 (m-40) cc_final: 0.8647 (m-40) REVERT: D 574 LEU cc_start: 0.9127 (mt) cc_final: 0.8910 (mt) REVERT: D 576 MET cc_start: 0.9152 (ppp) cc_final: 0.8816 (ppp) REVERT: D 581 MET cc_start: 0.8819 (mtm) cc_final: 0.8101 (mtm) REVERT: D 620 MET cc_start: 0.9700 (ptp) cc_final: 0.9492 (ptp) REVERT: D 636 ARG cc_start: 0.8519 (mmp-170) cc_final: 0.8046 (mmm160) REVERT: D 706 MET cc_start: 0.8529 (ptm) cc_final: 0.8310 (pmm) REVERT: D 707 ILE cc_start: 0.9383 (tt) cc_final: 0.9138 (tt) REVERT: D 757 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8942 (tm-30) REVERT: D 780 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8852 (mm-30) REVERT: D 784 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9009 (mm-30) REVERT: D 800 ILE cc_start: 0.9355 (tp) cc_final: 0.9047 (tp) REVERT: D 804 ASP cc_start: 0.8685 (m-30) cc_final: 0.8466 (p0) REVERT: D 844 LEU cc_start: 0.8671 (mm) cc_final: 0.7732 (tp) REVERT: D 854 HIS cc_start: 0.9030 (m-70) cc_final: 0.8747 (m-70) REVERT: D 862 ASP cc_start: 0.9005 (t0) cc_final: 0.8732 (t0) REVERT: D 866 ARG cc_start: 0.9189 (ptt180) cc_final: 0.8566 (ptp-170) REVERT: D 928 ASP cc_start: 0.8719 (p0) cc_final: 0.8400 (p0) REVERT: D 990 ASP cc_start: 0.8272 (m-30) cc_final: 0.8066 (m-30) REVERT: D 1001 GLN cc_start: 0.9484 (tt0) cc_final: 0.9282 (tt0) REVERT: D 1028 LEU cc_start: 0.9650 (tp) cc_final: 0.9356 (tp) REVERT: D 1032 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9136 (tm-30) REVERT: D 1036 GLU cc_start: 0.8524 (tp30) cc_final: 0.7650 (tt0) REVERT: D 1112 MET cc_start: 0.9224 (tpt) cc_final: 0.8950 (tpp) REVERT: D 1139 GLN cc_start: 0.9266 (tp-100) cc_final: 0.8845 (tp-100) REVERT: D 1151 ASP cc_start: 0.8448 (t0) cc_final: 0.8035 (t0) REVERT: D 1248 LEU cc_start: 0.9372 (mp) cc_final: 0.9036 (mp) REVERT: D 1250 GLU cc_start: 0.8760 (mp0) cc_final: 0.7220 (pp20) REVERT: D 1267 TYR cc_start: 0.8748 (m-80) cc_final: 0.8463 (m-10) REVERT: D 1272 VAL cc_start: 0.8731 (t) cc_final: 0.8432 (p) REVERT: E 43 LEU cc_start: 0.9715 (mm) cc_final: 0.9496 (mm) REVERT: E 65 ASN cc_start: 0.9208 (t0) cc_final: 0.8892 (t0) REVERT: E 66 ASP cc_start: 0.8767 (m-30) cc_final: 0.8548 (m-30) REVERT: E 67 TYR cc_start: 0.9181 (t80) cc_final: 0.8972 (t80) REVERT: E 78 TYR cc_start: 0.8525 (m-10) cc_final: 0.8210 (m-10) REVERT: E 79 VAL cc_start: 0.9228 (t) cc_final: 0.8879 (m) REVERT: E 97 ARG cc_start: 0.9521 (mtp-110) cc_final: 0.9252 (mtm110) REVERT: E 103 LEU cc_start: 0.9257 (mt) cc_final: 0.9016 (mt) REVERT: F 252 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8625 (mmm160) REVERT: F 258 TYR cc_start: 0.9191 (t80) cc_final: 0.8922 (t80) REVERT: F 308 LYS cc_start: 0.9470 (pttp) cc_final: 0.9194 (mmmt) REVERT: F 315 MET cc_start: 0.6757 (mpp) cc_final: 0.6544 (mpp) REVERT: F 333 GLU cc_start: 0.8272 (tt0) cc_final: 0.7788 (tm-30) REVERT: F 357 ARG cc_start: 0.9649 (tmt170) cc_final: 0.9294 (tpt90) REVERT: F 372 MET cc_start: 0.9592 (mmp) cc_final: 0.9316 (mmm) REVERT: F 501 GLU cc_start: 0.8767 (mp0) cc_final: 0.8372 (tp30) REVERT: J 55 LEU cc_start: 0.9106 (tp) cc_final: 0.8800 (tp) REVERT: J 84 MET cc_start: 0.9484 (mpp) cc_final: 0.9152 (mpp) REVERT: J 86 LEU cc_start: 0.9621 (tp) cc_final: 0.9301 (mt) REVERT: J 91 ILE cc_start: 0.8821 (pt) cc_final: 0.8460 (pt) REVERT: M 156 GLU cc_start: 0.9704 (tm-30) cc_final: 0.9465 (mm-30) outliers start: 3 outliers final: 2 residues processed: 956 average time/residue: 0.1985 time to fit residues: 298.0711 Evaluate side-chains 803 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 801 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 179 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 318 optimal weight: 8.9990 chunk 185 optimal weight: 0.0570 chunk 228 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS D 410 GLN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN D1160 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.109212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079201 restraints weight = 99888.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080236 restraints weight = 53492.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080385 restraints weight = 36444.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081784 restraints weight = 31256.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.081720 restraints weight = 24308.843| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30158 Z= 0.209 Angle : 0.796 24.490 41380 Z= 0.413 Chirality : 0.055 1.908 4726 Planarity : 0.008 0.365 5007 Dihedral : 17.586 177.500 5172 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3441 helix: 0.11 (0.13), residues: 1402 sheet: -0.82 (0.25), residues: 393 loop : -1.31 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 482 TYR 0.029 0.002 TYR D 793 PHE 0.023 0.002 PHE C 977 TRP 0.041 0.002 TRP M 112 HIS 0.011 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (30150) covalent geometry : angle 0.78907 / 0.41 (41368) hydrogen bonds : bond 0.04951 / 3.36 ( 1389) hydrogen bonds : angle 5.45615 / 3.82 ( 3855) metal coordination : bond 0.01208 / 0.55 ( 8) metal coordination : angle 6.41595 / 4.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 948 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8875 (tp30) cc_final: 0.8583 (tp30) REVERT: A 30 PHE cc_start: 0.7999 (m-10) cc_final: 0.7689 (m-80) REVERT: A 34 LEU cc_start: 0.9388 (tp) cc_final: 0.8998 (tp) REVERT: A 138 LEU cc_start: 0.9384 (mp) cc_final: 0.9008 (mp) REVERT: A 197 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7998 (mp0) REVERT: A 208 LEU cc_start: 0.9605 (mm) cc_final: 0.9356 (mm) REVERT: A 219 PHE cc_start: 0.8239 (m-80) cc_final: 0.7758 (m-80) REVERT: B 12 ASP cc_start: 0.9271 (t70) cc_final: 0.9048 (t0) REVERT: B 20 GLN cc_start: 0.8705 (mp10) cc_final: 0.8059 (mp10) REVERT: B 30 PHE cc_start: 0.9547 (m-80) cc_final: 0.9285 (m-80) REVERT: B 40 ARG cc_start: 0.9141 (mmp-170) cc_final: 0.8797 (mmm160) REVERT: B 42 LEU cc_start: 0.9813 (mt) cc_final: 0.9588 (mt) REVERT: B 120 ASN cc_start: 0.9441 (t0) cc_final: 0.8981 (t0) REVERT: B 151 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8723 (tm-30) REVERT: B 165 ASP cc_start: 0.9013 (m-30) cc_final: 0.8691 (m-30) REVERT: B 177 LYS cc_start: 0.8449 (mppt) cc_final: 0.8192 (mmtm) REVERT: B 213 LYS cc_start: 0.9581 (tptp) cc_final: 0.9350 (tppt) REVERT: B 217 GLU cc_start: 0.9511 (pt0) cc_final: 0.9188 (tm-30) REVERT: B 219 PHE cc_start: 0.9313 (m-80) cc_final: 0.9054 (m-80) REVERT: C 91 TYR cc_start: 0.9271 (t80) cc_final: 0.9063 (t80) REVERT: C 127 MET cc_start: 0.8778 (tmm) cc_final: 0.8299 (tmm) REVERT: C 275 LEU cc_start: 0.9428 (tt) cc_final: 0.9191 (mt) REVERT: C 439 PHE cc_start: 0.9227 (t80) cc_final: 0.8677 (t80) REVERT: C 466 GLU cc_start: 0.9323 (pm20) cc_final: 0.9093 (pm20) REVERT: C 482 ARG cc_start: 0.8691 (mtt90) cc_final: 0.7625 (mpt-90) REVERT: C 483 MET cc_start: 0.8734 (tpp) cc_final: 0.8147 (tpp) REVERT: C 511 PHE cc_start: 0.8882 (m-80) cc_final: 0.8029 (m-10) REVERT: C 543 GLN cc_start: 0.8136 (tt0) cc_final: 0.7224 (tt0) REVERT: C 585 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8029 (tp-100) REVERT: C 601 ASP cc_start: 0.9249 (t0) cc_final: 0.8798 (p0) REVERT: C 620 ARG cc_start: 0.9262 (tpm170) cc_final: 0.8885 (tpm170) REVERT: C 672 MET cc_start: 0.7197 (ppp) cc_final: 0.6732 (ppp) REVERT: C 818 GLU cc_start: 0.9602 (tp30) cc_final: 0.9345 (tm-30) REVERT: C 839 VAL cc_start: 0.9253 (t) cc_final: 0.8966 (t) REVERT: C 846 LYS cc_start: 0.9196 (tptt) cc_final: 0.8772 (tppt) REVERT: C 873 VAL cc_start: 0.9171 (t) cc_final: 0.8897 (p) REVERT: C 892 LYS cc_start: 0.9200 (ptpt) cc_final: 0.8776 (ptpt) REVERT: C 926 MET cc_start: 0.9004 (tpt) cc_final: 0.8419 (tpp) REVERT: C 933 GLU cc_start: 0.8838 (tt0) cc_final: 0.8579 (tt0) REVERT: C 944 TRP cc_start: 0.8699 (p90) cc_final: 0.8172 (p90) REVERT: C 962 GLU cc_start: 0.8520 (mp0) cc_final: 0.8283 (mp0) REVERT: C 1039 ASP cc_start: 0.9247 (m-30) cc_final: 0.8860 (m-30) REVERT: C 1040 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7874 (mptt) REVERT: C 1077 GLN cc_start: 0.9432 (mt0) cc_final: 0.9139 (mt0) REVERT: C 1090 THR cc_start: 0.9021 (m) cc_final: 0.8768 (p) REVERT: C 1124 LEU cc_start: 0.9640 (tt) cc_final: 0.9349 (tt) REVERT: C 1127 GLU cc_start: 0.9079 (pp20) cc_final: 0.8777 (pp20) REVERT: C 1128 LEU cc_start: 0.9461 (mt) cc_final: 0.9169 (mt) REVERT: D 10 LEU cc_start: 0.9229 (tp) cc_final: 0.9013 (tp) REVERT: D 29 LYS cc_start: 0.9209 (ptpp) cc_final: 0.8877 (ptpp) REVERT: D 33 THR cc_start: 0.8977 (p) cc_final: 0.8316 (p) REVERT: D 52 PHE cc_start: 0.8094 (m-80) cc_final: 0.6973 (m-10) REVERT: D 66 LYS cc_start: 0.9257 (ptpp) cc_final: 0.8975 (mmmt) REVERT: D 92 MET cc_start: 0.8345 (mmm) cc_final: 0.8125 (mmm) REVERT: D 105 TRP cc_start: 0.9152 (m-10) cc_final: 0.8368 (m100) REVERT: D 118 LEU cc_start: 0.9369 (mm) cc_final: 0.8958 (mm) REVERT: D 119 ASP cc_start: 0.8501 (t70) cc_final: 0.8227 (t0) REVERT: D 120 LEU cc_start: 0.8937 (mm) cc_final: 0.8460 (tp) REVERT: D 205 MET cc_start: 0.9029 (mmm) cc_final: 0.8455 (mmp) REVERT: D 244 LEU cc_start: 0.9776 (mt) cc_final: 0.9550 (mt) REVERT: D 252 PHE cc_start: 0.8260 (p90) cc_final: 0.8043 (p90) REVERT: D 256 MET cc_start: 0.7652 (tpp) cc_final: 0.6852 (tpp) REVERT: D 262 GLN cc_start: 0.9535 (tt0) cc_final: 0.9002 (tm-30) REVERT: D 341 ASN cc_start: 0.8937 (m-40) cc_final: 0.8613 (m-40) REVERT: D 345 ARG cc_start: 0.8792 (ttt-90) cc_final: 0.8515 (ttt180) REVERT: D 346 ARG cc_start: 0.9242 (ttm110) cc_final: 0.8375 (ptp-110) REVERT: D 397 ARG cc_start: 0.8568 (tmm-80) cc_final: 0.8268 (tmm-80) REVERT: D 400 LYS cc_start: 0.9540 (mmpt) cc_final: 0.9281 (mmpt) REVERT: D 427 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: D 471 SER cc_start: 0.9278 (t) cc_final: 0.8646 (p) REVERT: D 475 MET cc_start: 0.8946 (mmp) cc_final: 0.8680 (mmp) REVERT: D 504 LEU cc_start: 0.9300 (tp) cc_final: 0.9005 (tp) REVERT: D 510 GLN cc_start: 0.8078 (mp10) cc_final: 0.7680 (mp10) REVERT: D 515 MET cc_start: 0.8603 (mmp) cc_final: 0.8311 (mmm) REVERT: D 527 LEU cc_start: 0.9381 (mt) cc_final: 0.9127 (mt) REVERT: D 532 PHE cc_start: 0.7833 (m-10) cc_final: 0.7242 (m-80) REVERT: D 560 LEU cc_start: 0.9526 (tp) cc_final: 0.9303 (tp) REVERT: D 563 ASN cc_start: 0.8887 (m-40) cc_final: 0.8560 (m110) REVERT: D 574 LEU cc_start: 0.9077 (mt) cc_final: 0.8876 (mt) REVERT: D 576 MET cc_start: 0.9154 (ppp) cc_final: 0.8850 (ppp) REVERT: D 581 MET cc_start: 0.8837 (mtm) cc_final: 0.8346 (mtm) REVERT: D 706 MET cc_start: 0.8835 (ptm) cc_final: 0.8453 (pmm) REVERT: D 717 LYS cc_start: 0.9316 (tmmt) cc_final: 0.8584 (tmmt) REVERT: D 757 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8971 (tm-30) REVERT: D 780 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8871 (mm-30) REVERT: D 784 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9021 (mm-30) REVERT: D 800 ILE cc_start: 0.9352 (tp) cc_final: 0.8889 (tp) REVERT: D 804 ASP cc_start: 0.8622 (m-30) cc_final: 0.8217 (m-30) REVERT: D 840 PHE cc_start: 0.9070 (m-80) cc_final: 0.8540 (m-80) REVERT: D 844 LEU cc_start: 0.8687 (mm) cc_final: 0.7780 (tp) REVERT: D 854 HIS cc_start: 0.9051 (m-70) cc_final: 0.8734 (m-70) REVERT: D 862 ASP cc_start: 0.9059 (t0) cc_final: 0.8845 (t0) REVERT: D 866 ARG cc_start: 0.9218 (ptt180) cc_final: 0.8707 (ptm160) REVERT: D 928 ASP cc_start: 0.8780 (p0) cc_final: 0.8464 (p0) REVERT: D 1028 LEU cc_start: 0.9581 (tp) cc_final: 0.9146 (tp) REVERT: D 1032 GLN cc_start: 0.9401 (tm-30) cc_final: 0.9078 (tm-30) REVERT: D 1036 GLU cc_start: 0.8705 (tp30) cc_final: 0.7639 (tt0) REVERT: D 1139 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8865 (tp-100) REVERT: D 1151 ASP cc_start: 0.8455 (t0) cc_final: 0.8021 (t0) REVERT: D 1152 LYS cc_start: 0.9104 (ptmt) cc_final: 0.8804 (ttpt) REVERT: D 1231 ARG cc_start: 0.9367 (ptt180) cc_final: 0.8994 (ptt-90) REVERT: D 1267 TYR cc_start: 0.8759 (m-80) cc_final: 0.8456 (m-10) REVERT: D 1272 VAL cc_start: 0.8872 (t) cc_final: 0.8620 (m) REVERT: E 50 LYS cc_start: 0.9513 (mtpt) cc_final: 0.9125 (mtpt) REVERT: E 59 LYS cc_start: 0.9456 (ttpp) cc_final: 0.9141 (ptpt) REVERT: E 65 ASN cc_start: 0.9165 (t0) cc_final: 0.8894 (t0) REVERT: E 66 ASP cc_start: 0.8773 (m-30) cc_final: 0.8321 (m-30) REVERT: E 79 VAL cc_start: 0.9228 (t) cc_final: 0.8934 (m) REVERT: E 97 ARG cc_start: 0.9520 (mtp-110) cc_final: 0.9217 (mtm110) REVERT: F 252 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8592 (mmm160) REVERT: F 258 TYR cc_start: 0.9182 (t80) cc_final: 0.8917 (t80) REVERT: F 263 MET cc_start: 0.8613 (mmp) cc_final: 0.8412 (mmm) REVERT: F 326 LEU cc_start: 0.9177 (mm) cc_final: 0.8969 (mm) REVERT: F 349 TRP cc_start: 0.7993 (m-10) cc_final: 0.7001 (m-10) REVERT: F 352 ARG cc_start: 0.8844 (mtp-110) cc_final: 0.8518 (mtm180) REVERT: F 357 ARG cc_start: 0.9633 (tmt170) cc_final: 0.9285 (tpt90) REVERT: F 372 MET cc_start: 0.9569 (mmp) cc_final: 0.9271 (mmm) REVERT: F 441 ASP cc_start: 0.8215 (t0) cc_final: 0.7722 (t0) REVERT: J 84 MET cc_start: 0.9405 (mpp) cc_final: 0.9167 (mpp) REVERT: J 86 LEU cc_start: 0.9614 (tp) cc_final: 0.9295 (mt) REVERT: J 91 ILE cc_start: 0.8792 (pt) cc_final: 0.8424 (pt) REVERT: M 71 PHE cc_start: 0.9291 (m-10) cc_final: 0.9067 (m-80) REVERT: M 156 GLU cc_start: 0.9708 (tm-30) cc_final: 0.9448 (mm-30) outliers start: 4 outliers final: 0 residues processed: 949 average time/residue: 0.2021 time to fit residues: 299.2492 Evaluate side-chains 775 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 775 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 33 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 296 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN D1110 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.107249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075503 restraints weight = 99934.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077547 restraints weight = 56961.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079027 restraints weight = 35676.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079414 restraints weight = 28323.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079890 restraints weight = 24932.462| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 30158 Z= 0.238 Angle : 0.801 24.640 41380 Z= 0.416 Chirality : 0.055 1.901 4726 Planarity : 0.008 0.350 5007 Dihedral : 17.657 177.952 5172 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3441 helix: 0.05 (0.13), residues: 1409 sheet: -0.84 (0.26), residues: 384 loop : -1.35 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 159 TYR 0.027 0.002 TYR F 526 PHE 0.022 0.002 PHE D 760 TRP 0.055 0.002 TRP M 112 HIS 0.012 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (30150) covalent geometry : angle 0.79492 / 0.42 (41368) hydrogen bonds : bond 0.04918 / 3.29 ( 1389) hydrogen bonds : angle 5.50577 / 3.86 ( 3855) metal coordination : bond 0.01174 / 0.47 ( 8) metal coordination : angle 5.83500 / 3.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 903 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7978 (m-10) cc_final: 0.7195 (m-80) REVERT: A 34 LEU cc_start: 0.9394 (tp) cc_final: 0.8988 (tp) REVERT: A 78 LEU cc_start: 0.9523 (pp) cc_final: 0.9265 (pp) REVERT: A 83 LEU cc_start: 0.9674 (tp) cc_final: 0.9449 (mm) REVERT: A 138 LEU cc_start: 0.9369 (mp) cc_final: 0.9061 (mp) REVERT: A 197 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7855 (mp0) REVERT: A 219 PHE cc_start: 0.8313 (m-80) cc_final: 0.7832 (m-80) REVERT: B 9 LEU cc_start: 0.7944 (pt) cc_final: 0.7706 (pp) REVERT: B 12 ASP cc_start: 0.9306 (t70) cc_final: 0.9096 (t0) REVERT: B 14 LEU cc_start: 0.9187 (mt) cc_final: 0.8659 (mt) REVERT: B 20 GLN cc_start: 0.8712 (mp10) cc_final: 0.8082 (mp10) REVERT: B 30 PHE cc_start: 0.9582 (m-80) cc_final: 0.9307 (m-80) REVERT: B 40 ARG cc_start: 0.9181 (mmp-170) cc_final: 0.8939 (mmm160) REVERT: B 42 LEU cc_start: 0.9821 (mt) cc_final: 0.9603 (mt) REVERT: B 44 SER cc_start: 0.9572 (m) cc_final: 0.9370 (p) REVERT: B 120 ASN cc_start: 0.9446 (t0) cc_final: 0.9011 (t0) REVERT: B 151 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8738 (tm-30) REVERT: B 177 LYS cc_start: 0.8588 (mppt) cc_final: 0.8279 (mmtm) REVERT: B 213 LYS cc_start: 0.9584 (tptp) cc_final: 0.9364 (tppt) REVERT: B 217 GLU cc_start: 0.9502 (pt0) cc_final: 0.9198 (tm-30) REVERT: B 219 PHE cc_start: 0.9368 (m-80) cc_final: 0.9116 (m-80) REVERT: C 91 TYR cc_start: 0.9292 (t80) cc_final: 0.9058 (t80) REVERT: C 127 MET cc_start: 0.8397 (tmm) cc_final: 0.8084 (tmm) REVERT: C 279 ARG cc_start: 0.9631 (tmt170) cc_final: 0.9372 (ttp80) REVERT: C 387 ASN cc_start: 0.9148 (m110) cc_final: 0.8814 (m-40) REVERT: C 439 PHE cc_start: 0.9171 (t80) cc_final: 0.8630 (t80) REVERT: C 441 ASP cc_start: 0.8951 (m-30) cc_final: 0.8715 (m-30) REVERT: C 466 GLU cc_start: 0.9295 (pm20) cc_final: 0.9077 (pm20) REVERT: C 482 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8202 (mpt180) REVERT: C 483 MET cc_start: 0.8745 (tpp) cc_final: 0.8324 (tpp) REVERT: C 511 PHE cc_start: 0.9036 (m-80) cc_final: 0.8211 (m-10) REVERT: C 543 GLN cc_start: 0.8097 (tt0) cc_final: 0.7387 (tt0) REVERT: C 562 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7949 (mtm180) REVERT: C 585 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8226 (tp40) REVERT: C 598 GLU cc_start: 0.9466 (pm20) cc_final: 0.9181 (pm20) REVERT: C 601 ASP cc_start: 0.9280 (t0) cc_final: 0.8808 (p0) REVERT: C 620 ARG cc_start: 0.9309 (tpm170) cc_final: 0.8752 (tpm170) REVERT: C 651 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8019 (mt-10) REVERT: C 672 MET cc_start: 0.7571 (ppp) cc_final: 0.7064 (ppp) REVERT: C 744 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8884 (mp0) REVERT: C 818 GLU cc_start: 0.9605 (tp30) cc_final: 0.9335 (tm-30) REVERT: C 846 LYS cc_start: 0.9203 (tptt) cc_final: 0.8842 (tppt) REVERT: C 873 VAL cc_start: 0.9195 (t) cc_final: 0.8878 (p) REVERT: C 889 HIS cc_start: 0.8100 (m90) cc_final: 0.7866 (m90) REVERT: C 892 LYS cc_start: 0.9198 (ptpt) cc_final: 0.8774 (ptpt) REVERT: C 904 MET cc_start: 0.9275 (tpp) cc_final: 0.8974 (tpp) REVERT: C 926 MET cc_start: 0.8993 (tpt) cc_final: 0.8459 (tpp) REVERT: C 930 GLN cc_start: 0.9396 (pt0) cc_final: 0.9175 (pt0) REVERT: C 933 GLU cc_start: 0.8919 (tt0) cc_final: 0.8679 (tt0) REVERT: C 944 TRP cc_start: 0.8764 (p90) cc_final: 0.8179 (p90) REVERT: C 962 GLU cc_start: 0.8552 (mp0) cc_final: 0.8268 (mp0) REVERT: C 1039 ASP cc_start: 0.9301 (m-30) cc_final: 0.8971 (m-30) REVERT: C 1040 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7802 (mptt) REVERT: C 1071 MET cc_start: 0.7584 (pmm) cc_final: 0.6684 (pmm) REVERT: C 1076 MET cc_start: 0.9272 (mtp) cc_final: 0.8677 (ttm) REVERT: C 1077 GLN cc_start: 0.9461 (mt0) cc_final: 0.9144 (mt0) REVERT: C 1085 LEU cc_start: 0.9690 (tt) cc_final: 0.9486 (tt) REVERT: C 1090 THR cc_start: 0.9001 (m) cc_final: 0.8713 (p) REVERT: C 1121 PHE cc_start: 0.9463 (t80) cc_final: 0.9159 (t80) REVERT: C 1127 GLU cc_start: 0.9053 (pp20) cc_final: 0.8851 (pp20) REVERT: C 1128 LEU cc_start: 0.9388 (mt) cc_final: 0.9144 (mt) REVERT: C 1133 LEU cc_start: 0.9367 (mt) cc_final: 0.9133 (mt) REVERT: D 29 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8941 (ptpp) REVERT: D 52 PHE cc_start: 0.8159 (m-80) cc_final: 0.7109 (m-10) REVERT: D 66 LYS cc_start: 0.9318 (ptpp) cc_final: 0.8942 (mmmt) REVERT: D 105 TRP cc_start: 0.9194 (m-10) cc_final: 0.8449 (m100) REVERT: D 118 LEU cc_start: 0.9377 (mm) cc_final: 0.8956 (mm) REVERT: D 119 ASP cc_start: 0.8466 (t70) cc_final: 0.8139 (t0) REVERT: D 120 LEU cc_start: 0.8893 (mm) cc_final: 0.8380 (tp) REVERT: D 205 MET cc_start: 0.9011 (mmm) cc_final: 0.8599 (mmp) REVERT: D 262 GLN cc_start: 0.9543 (tt0) cc_final: 0.9023 (tm-30) REVERT: D 341 ASN cc_start: 0.8914 (m-40) cc_final: 0.8609 (m-40) REVERT: D 346 ARG cc_start: 0.9266 (ttm110) cc_final: 0.8498 (ptp-110) REVERT: D 378 VAL cc_start: 0.9680 (t) cc_final: 0.9444 (p) REVERT: D 423 ASP cc_start: 0.8833 (p0) cc_final: 0.8565 (p0) REVERT: D 424 TYR cc_start: 0.8780 (m-80) cc_final: 0.8336 (m-10) REVERT: D 427 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: D 436 LEU cc_start: 0.8953 (mm) cc_final: 0.8547 (tp) REVERT: D 471 SER cc_start: 0.9228 (t) cc_final: 0.8433 (m) REVERT: D 475 MET cc_start: 0.8977 (mmp) cc_final: 0.8724 (mmp) REVERT: D 503 THR cc_start: 0.8589 (p) cc_final: 0.8041 (p) REVERT: D 504 LEU cc_start: 0.9231 (tp) cc_final: 0.8932 (tp) REVERT: D 515 MET cc_start: 0.8622 (mmp) cc_final: 0.8345 (mmm) REVERT: D 532 PHE cc_start: 0.8060 (m-10) cc_final: 0.7768 (m-80) REVERT: D 556 ARG cc_start: 0.8759 (ttt90) cc_final: 0.8505 (ttt180) REVERT: D 560 LEU cc_start: 0.9527 (tp) cc_final: 0.9297 (tp) REVERT: D 563 ASN cc_start: 0.8997 (m-40) cc_final: 0.8629 (m110) REVERT: D 574 LEU cc_start: 0.9062 (mt) cc_final: 0.8856 (mt) REVERT: D 576 MET cc_start: 0.9181 (ppp) cc_final: 0.8868 (ppp) REVERT: D 581 MET cc_start: 0.8893 (mtm) cc_final: 0.8478 (mtm) REVERT: D 665 GLU cc_start: 0.9227 (pm20) cc_final: 0.8993 (pm20) REVERT: D 667 THR cc_start: 0.9371 (p) cc_final: 0.9162 (t) REVERT: D 706 MET cc_start: 0.8823 (ptm) cc_final: 0.8457 (pmm) REVERT: D 717 LYS cc_start: 0.9344 (tmmt) cc_final: 0.8970 (tmmt) REVERT: D 757 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8869 (tm-30) REVERT: D 780 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8409 (tt0) REVERT: D 784 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8993 (mm-30) REVERT: D 800 ILE cc_start: 0.9395 (tp) cc_final: 0.9007 (tp) REVERT: D 844 LEU cc_start: 0.8810 (mm) cc_final: 0.7936 (tp) REVERT: D 854 HIS cc_start: 0.9034 (m-70) cc_final: 0.8722 (m-70) REVERT: D 862 ASP cc_start: 0.9125 (t0) cc_final: 0.8877 (t0) REVERT: D 866 ARG cc_start: 0.9277 (ptt180) cc_final: 0.8684 (ptm160) REVERT: D 869 ASP cc_start: 0.9017 (t70) cc_final: 0.8657 (t0) REVERT: D 928 ASP cc_start: 0.8736 (p0) cc_final: 0.8427 (p0) REVERT: D 962 VAL cc_start: 0.9285 (m) cc_final: 0.9031 (p) REVERT: D 1028 LEU cc_start: 0.9591 (tp) cc_final: 0.9360 (tp) REVERT: D 1036 GLU cc_start: 0.8751 (tp30) cc_final: 0.8122 (tp30) REVERT: D 1133 HIS cc_start: 0.9249 (t70) cc_final: 0.8830 (t70) REVERT: D 1139 GLN cc_start: 0.9273 (tp-100) cc_final: 0.8811 (tp-100) REVERT: D 1151 ASP cc_start: 0.8568 (t0) cc_final: 0.8197 (t0) REVERT: D 1231 ARG cc_start: 0.9352 (ptt180) cc_final: 0.8984 (ptt-90) REVERT: E 35 ILE cc_start: 0.8678 (mm) cc_final: 0.8085 (mm) REVERT: E 46 ARG cc_start: 0.9206 (mmp80) cc_final: 0.8924 (mtt90) REVERT: E 50 LYS cc_start: 0.9529 (mtpt) cc_final: 0.9196 (mtpt) REVERT: E 65 ASN cc_start: 0.9145 (t0) cc_final: 0.8897 (t0) REVERT: E 66 ASP cc_start: 0.8749 (m-30) cc_final: 0.8336 (m-30) REVERT: E 78 TYR cc_start: 0.8472 (m-10) cc_final: 0.8239 (m-10) REVERT: E 79 VAL cc_start: 0.9338 (t) cc_final: 0.8880 (m) REVERT: E 97 ARG cc_start: 0.9534 (mtp-110) cc_final: 0.9226 (mtm110) REVERT: E 99 ILE cc_start: 0.9671 (mp) cc_final: 0.9471 (mp) REVERT: F 213 ARG cc_start: 0.8699 (ppt170) cc_final: 0.8156 (ttp80) REVERT: F 252 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8597 (mmm160) REVERT: F 258 TYR cc_start: 0.9209 (t80) cc_final: 0.8897 (t80) REVERT: F 315 MET cc_start: 0.7058 (mpp) cc_final: 0.6522 (mpp) REVERT: F 349 TRP cc_start: 0.8101 (m-10) cc_final: 0.7791 (t60) REVERT: F 357 ARG cc_start: 0.9648 (tmt170) cc_final: 0.9301 (tpt90) REVERT: F 372 MET cc_start: 0.9552 (mmp) cc_final: 0.9294 (mmm) REVERT: F 441 ASP cc_start: 0.8348 (t0) cc_final: 0.7839 (t0) REVERT: F 501 GLU cc_start: 0.8841 (mp0) cc_final: 0.8466 (tp30) REVERT: J 84 MET cc_start: 0.9329 (mpp) cc_final: 0.9118 (mpp) REVERT: J 86 LEU cc_start: 0.9637 (tp) cc_final: 0.9320 (mt) REVERT: J 91 ILE cc_start: 0.8837 (pt) cc_final: 0.8512 (pt) REVERT: M 71 PHE cc_start: 0.9300 (m-10) cc_final: 0.9048 (m-80) REVERT: M 156 GLU cc_start: 0.9723 (tm-30) cc_final: 0.9443 (mm-30) outliers start: 1 outliers final: 0 residues processed: 903 average time/residue: 0.2062 time to fit residues: 291.7907 Evaluate side-chains 765 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 765 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 286 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 289 optimal weight: 30.0000 chunk 269 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 505 HIS ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 882 GLN D1139 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.108273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078056 restraints weight = 100902.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078488 restraints weight = 57869.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079786 restraints weight = 36844.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080408 restraints weight = 29860.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080590 restraints weight = 25558.539| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30158 Z= 0.193 Angle : 0.779 24.463 41380 Z= 0.406 Chirality : 0.055 1.912 4726 Planarity : 0.008 0.353 5007 Dihedral : 17.649 177.826 5172 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3441 helix: 0.12 (0.13), residues: 1397 sheet: -0.75 (0.27), residues: 374 loop : -1.36 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 18 TYR 0.026 0.002 TYR E 56 PHE 0.028 0.002 PHE C 166 TRP 0.056 0.002 TRP M 112 HIS 0.011 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (30150) covalent geometry : angle 0.77461 / 0.41 (41368) hydrogen bonds : bond 0.04644 / 3.11 ( 1389) hydrogen bonds : angle 5.39326 / 3.79 ( 3855) metal coordination : bond 0.00992 / 0.39 ( 8) metal coordination : angle 5.12647 / 3.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 886 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9425 (tp) cc_final: 0.9009 (tp) REVERT: A 38 LEU cc_start: 0.9767 (mt) cc_final: 0.9560 (mt) REVERT: A 83 LEU cc_start: 0.9659 (tp) cc_final: 0.9453 (mm) REVERT: A 138 LEU cc_start: 0.9343 (mp) cc_final: 0.9073 (mp) REVERT: A 197 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8017 (mp0) REVERT: A 208 LEU cc_start: 0.9556 (mm) cc_final: 0.9320 (mm) REVERT: A 219 PHE cc_start: 0.8292 (m-80) cc_final: 0.7788 (m-80) REVERT: B 12 ASP cc_start: 0.9270 (t70) cc_final: 0.8733 (t0) REVERT: B 14 LEU cc_start: 0.9228 (mt) cc_final: 0.9025 (mt) REVERT: B 20 GLN cc_start: 0.8584 (mp10) cc_final: 0.7691 (mp10) REVERT: B 30 PHE cc_start: 0.9551 (m-80) cc_final: 0.9272 (m-80) REVERT: B 40 ARG cc_start: 0.9182 (mmp-170) cc_final: 0.8645 (mmm160) REVERT: B 42 LEU cc_start: 0.9810 (mt) cc_final: 0.9602 (mt) REVERT: B 120 ASN cc_start: 0.9456 (t0) cc_final: 0.9058 (t0) REVERT: B 151 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8788 (tm-30) REVERT: B 177 LYS cc_start: 0.8563 (mppt) cc_final: 0.8329 (mmtm) REVERT: B 213 LYS cc_start: 0.9581 (tptp) cc_final: 0.9378 (tppt) REVERT: B 217 GLU cc_start: 0.9479 (pt0) cc_final: 0.9180 (tm-30) REVERT: B 219 PHE cc_start: 0.9316 (m-80) cc_final: 0.9079 (m-80) REVERT: C 91 TYR cc_start: 0.9286 (t80) cc_final: 0.9024 (t80) REVERT: C 289 LYS cc_start: 0.9716 (mttt) cc_final: 0.9497 (mmtp) REVERT: C 306 TYR cc_start: 0.8690 (t80) cc_final: 0.8305 (t80) REVERT: C 439 PHE cc_start: 0.9172 (t80) cc_final: 0.8632 (t80) REVERT: C 466 GLU cc_start: 0.9309 (pm20) cc_final: 0.9070 (pm20) REVERT: C 483 MET cc_start: 0.8595 (tpp) cc_final: 0.8126 (tpp) REVERT: C 511 PHE cc_start: 0.9004 (m-80) cc_final: 0.8137 (m-10) REVERT: C 536 GLU cc_start: 0.8876 (pt0) cc_final: 0.8635 (pt0) REVERT: C 543 GLN cc_start: 0.7946 (tt0) cc_final: 0.7158 (tt0) REVERT: C 585 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8297 (tp-100) REVERT: C 601 ASP cc_start: 0.9215 (t0) cc_final: 0.8807 (p0) REVERT: C 607 MET cc_start: 0.8544 (mtm) cc_final: 0.8342 (mtm) REVERT: C 620 ARG cc_start: 0.9324 (tpm170) cc_final: 0.8763 (tpm170) REVERT: C 713 MET cc_start: 0.8810 (tpp) cc_final: 0.8451 (ptp) REVERT: C 744 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8900 (mp0) REVERT: C 818 GLU cc_start: 0.9602 (tp30) cc_final: 0.9348 (tm-30) REVERT: C 846 LYS cc_start: 0.9231 (tptt) cc_final: 0.8824 (tppt) REVERT: C 889 HIS cc_start: 0.8307 (m90) cc_final: 0.7861 (m90) REVERT: C 892 LYS cc_start: 0.9231 (ptpt) cc_final: 0.8820 (ptpt) REVERT: C 904 MET cc_start: 0.9301 (tpp) cc_final: 0.8922 (tpp) REVERT: C 930 GLN cc_start: 0.9422 (pt0) cc_final: 0.9137 (pt0) REVERT: C 933 GLU cc_start: 0.8860 (tt0) cc_final: 0.8571 (tt0) REVERT: C 944 TRP cc_start: 0.8772 (p90) cc_final: 0.8371 (p90) REVERT: C 962 GLU cc_start: 0.8559 (mp0) cc_final: 0.8262 (mp0) REVERT: C 1036 LEU cc_start: 0.9039 (mt) cc_final: 0.8799 (mt) REVERT: C 1039 ASP cc_start: 0.9319 (m-30) cc_final: 0.8956 (m-30) REVERT: C 1040 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7908 (mptt) REVERT: C 1071 MET cc_start: 0.7499 (pmm) cc_final: 0.6305 (pmm) REVERT: C 1076 MET cc_start: 0.9279 (mtp) cc_final: 0.8672 (ttm) REVERT: C 1077 GLN cc_start: 0.9463 (mt0) cc_final: 0.9086 (mt0) REVERT: C 1086 GLN cc_start: 0.9449 (pt0) cc_final: 0.9135 (pt0) REVERT: C 1090 THR cc_start: 0.9099 (m) cc_final: 0.8784 (p) REVERT: C 1091 ILE cc_start: 0.9128 (pt) cc_final: 0.8858 (pt) REVERT: C 1092 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8369 (mtpp) REVERT: C 1121 PHE cc_start: 0.9497 (t80) cc_final: 0.9253 (t80) REVERT: C 1127 GLU cc_start: 0.9036 (pp20) cc_final: 0.8814 (pp20) REVERT: C 1128 LEU cc_start: 0.9404 (mt) cc_final: 0.9160 (mt) REVERT: C 1131 LEU cc_start: 0.9595 (mt) cc_final: 0.9354 (mt) REVERT: C 1133 LEU cc_start: 0.9341 (mt) cc_final: 0.9117 (mt) REVERT: D 29 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8947 (ptpp) REVERT: D 52 PHE cc_start: 0.8165 (m-80) cc_final: 0.7148 (m-10) REVERT: D 66 LYS cc_start: 0.9281 (ptpp) cc_final: 0.9059 (mmmm) REVERT: D 92 MET cc_start: 0.8432 (mmm) cc_final: 0.7898 (tpt) REVERT: D 105 TRP cc_start: 0.9153 (m-10) cc_final: 0.8381 (m100) REVERT: D 118 LEU cc_start: 0.9324 (mm) cc_final: 0.8864 (mm) REVERT: D 119 ASP cc_start: 0.8429 (t70) cc_final: 0.8084 (t0) REVERT: D 120 LEU cc_start: 0.8821 (mm) cc_final: 0.8379 (tp) REVERT: D 262 GLN cc_start: 0.9530 (tt0) cc_final: 0.9019 (tp-100) REVERT: D 310 MET cc_start: 0.9196 (mmp) cc_final: 0.8707 (mmp) REVERT: D 341 ASN cc_start: 0.8927 (m-40) cc_final: 0.8551 (m110) REVERT: D 346 ARG cc_start: 0.9275 (ttm110) cc_final: 0.8471 (ptp-110) REVERT: D 356 ARG cc_start: 0.9473 (mtm180) cc_final: 0.9107 (mtm180) REVERT: D 364 GLU cc_start: 0.9018 (pp20) cc_final: 0.8454 (pp20) REVERT: D 386 ARG cc_start: 0.8035 (tpt170) cc_final: 0.7619 (mmm160) REVERT: D 424 TYR cc_start: 0.8734 (m-80) cc_final: 0.8496 (m-10) REVERT: D 427 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.7567 (ttm-80) REVERT: D 475 MET cc_start: 0.8925 (mmp) cc_final: 0.8672 (mmp) REVERT: D 503 THR cc_start: 0.8463 (p) cc_final: 0.7629 (p) REVERT: D 506 ARG cc_start: 0.9373 (ttt180) cc_final: 0.8988 (tpt-90) REVERT: D 510 GLN cc_start: 0.8655 (mp10) cc_final: 0.8260 (mp10) REVERT: D 515 MET cc_start: 0.8649 (mmp) cc_final: 0.8369 (mmm) REVERT: D 523 GLN cc_start: 0.8755 (tt0) cc_final: 0.8139 (tp40) REVERT: D 554 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8538 (mt-10) REVERT: D 560 LEU cc_start: 0.9538 (tp) cc_final: 0.9336 (tp) REVERT: D 563 ASN cc_start: 0.9026 (m-40) cc_final: 0.8711 (m-40) REVERT: D 576 MET cc_start: 0.9096 (ppp) cc_final: 0.8860 (ppp) REVERT: D 581 MET cc_start: 0.8923 (mtm) cc_final: 0.8663 (mtm) REVERT: D 637 LEU cc_start: 0.9244 (mm) cc_final: 0.8899 (mm) REVERT: D 641 ARG cc_start: 0.9217 (tpt-90) cc_final: 0.8935 (tpp80) REVERT: D 646 ILE cc_start: 0.9734 (mm) cc_final: 0.9419 (mm) REVERT: D 667 THR cc_start: 0.9320 (p) cc_final: 0.9110 (t) REVERT: D 698 ASN cc_start: 0.9329 (t0) cc_final: 0.9119 (t0) REVERT: D 706 MET cc_start: 0.8900 (ptm) cc_final: 0.8517 (pmm) REVERT: D 717 LYS cc_start: 0.9400 (tmmt) cc_final: 0.8922 (tmmt) REVERT: D 757 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8912 (tm-30) REVERT: D 780 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8385 (tt0) REVERT: D 784 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8961 (mm-30) REVERT: D 840 PHE cc_start: 0.9026 (m-80) cc_final: 0.8723 (m-80) REVERT: D 844 LEU cc_start: 0.8709 (mm) cc_final: 0.7807 (tp) REVERT: D 854 HIS cc_start: 0.9009 (m-70) cc_final: 0.8698 (m-70) REVERT: D 862 ASP cc_start: 0.9154 (t0) cc_final: 0.8949 (t0) REVERT: D 866 ARG cc_start: 0.9269 (ptt180) cc_final: 0.8735 (ptm160) REVERT: D 869 ASP cc_start: 0.9045 (t70) cc_final: 0.8647 (t0) REVERT: D 872 TYR cc_start: 0.9018 (t80) cc_final: 0.8624 (t80) REVERT: D 928 ASP cc_start: 0.8727 (p0) cc_final: 0.8419 (p0) REVERT: D 962 VAL cc_start: 0.9272 (m) cc_final: 0.9015 (p) REVERT: D 981 ARG cc_start: 0.9019 (tmm160) cc_final: 0.8049 (tmm160) REVERT: D 1028 LEU cc_start: 0.9577 (tp) cc_final: 0.9312 (tp) REVERT: D 1030 ARG cc_start: 0.9494 (tpt170) cc_final: 0.9270 (tpp80) REVERT: D 1133 HIS cc_start: 0.9192 (t70) cc_final: 0.8831 (t70) REVERT: D 1139 GLN cc_start: 0.9263 (tp40) cc_final: 0.8863 (tp-100) REVERT: D 1151 ASP cc_start: 0.8581 (t0) cc_final: 0.8203 (t0) REVERT: D 1231 ARG cc_start: 0.9304 (ptt180) cc_final: 0.8913 (ptt-90) REVERT: E 35 ILE cc_start: 0.8756 (mm) cc_final: 0.8261 (mm) REVERT: E 43 LEU cc_start: 0.9645 (mm) cc_final: 0.9406 (mm) REVERT: E 50 LYS cc_start: 0.9519 (mtpt) cc_final: 0.9168 (mtpt) REVERT: E 59 LYS cc_start: 0.9330 (mtmm) cc_final: 0.9094 (ptmt) REVERT: E 65 ASN cc_start: 0.9206 (t0) cc_final: 0.8868 (t0) REVERT: E 66 ASP cc_start: 0.8885 (m-30) cc_final: 0.8570 (m-30) REVERT: E 97 ARG cc_start: 0.9517 (mtp-110) cc_final: 0.9208 (mtm110) REVERT: F 213 ARG cc_start: 0.8687 (ppt170) cc_final: 0.8105 (ttp80) REVERT: F 252 ARG cc_start: 0.9153 (mtp85) cc_final: 0.8593 (mmm160) REVERT: F 258 TYR cc_start: 0.9222 (t80) cc_final: 0.8907 (t80) REVERT: F 263 MET cc_start: 0.8661 (mmp) cc_final: 0.8307 (mmm) REVERT: F 282 MET cc_start: 0.9242 (pmm) cc_final: 0.8560 (pmm) REVERT: F 349 TRP cc_start: 0.7970 (m-10) cc_final: 0.7185 (t60) REVERT: F 352 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8471 (mtm180) REVERT: F 357 ARG cc_start: 0.9645 (tmt170) cc_final: 0.9306 (tpt90) REVERT: F 372 MET cc_start: 0.9564 (mmp) cc_final: 0.9300 (mmm) REVERT: F 441 ASP cc_start: 0.8458 (t0) cc_final: 0.8054 (t0) REVERT: F 501 GLU cc_start: 0.8735 (mp0) cc_final: 0.8425 (tp30) REVERT: J 84 MET cc_start: 0.9318 (mpp) cc_final: 0.9091 (mpp) REVERT: J 86 LEU cc_start: 0.9639 (tp) cc_final: 0.9326 (mt) REVERT: M 71 PHE cc_start: 0.9283 (m-10) cc_final: 0.9030 (m-80) REVERT: M 156 GLU cc_start: 0.9717 (tm-30) cc_final: 0.9433 (mm-30) outliers start: 2 outliers final: 1 residues processed: 887 average time/residue: 0.2005 time to fit residues: 277.9422 Evaluate side-chains 760 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 759 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 164 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 311 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 256 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS C 751 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 ASN D 882 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.110213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.079836 restraints weight = 97621.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081185 restraints weight = 57720.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082623 restraints weight = 34911.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082948 restraints weight = 27043.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.083864 restraints weight = 23781.275| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30158 Z= 0.157 Angle : 0.787 24.410 41380 Z= 0.405 Chirality : 0.055 1.924 4726 Planarity : 0.007 0.315 5007 Dihedral : 17.573 177.290 5172 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3441 helix: 0.14 (0.14), residues: 1393 sheet: -0.66 (0.27), residues: 375 loop : -1.31 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 118 TYR 0.025 0.002 TYR E 56 PHE 0.035 0.002 PHE C 214 TRP 0.062 0.002 TRP M 112 HIS 0.018 0.001 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (30150) covalent geometry : angle 0.77998 / 0.40 (41368) hydrogen bonds : bond 0.04492 / 3.04 ( 1389) hydrogen bonds : angle 5.27619 / 3.70 ( 3855) metal coordination : bond 0.02430 / 0.85 ( 8) metal coordination : angle 6.18458 / 4.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 909 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7647 (m-10) cc_final: 0.7300 (m-10) REVERT: A 34 LEU cc_start: 0.9419 (tp) cc_final: 0.9023 (tp) REVERT: A 38 LEU cc_start: 0.9769 (mt) cc_final: 0.9560 (mt) REVERT: A 83 LEU cc_start: 0.9668 (tp) cc_final: 0.9466 (mm) REVERT: A 125 ILE cc_start: 0.9535 (mm) cc_final: 0.9307 (mm) REVERT: A 138 LEU cc_start: 0.9414 (mp) cc_final: 0.9167 (mp) REVERT: A 151 GLN cc_start: 0.7943 (mp-120) cc_final: 0.7439 (pm20) REVERT: A 172 LEU cc_start: 0.9669 (mt) cc_final: 0.9452 (mt) REVERT: A 208 LEU cc_start: 0.9551 (mm) cc_final: 0.9293 (mm) REVERT: A 219 PHE cc_start: 0.8107 (m-80) cc_final: 0.7638 (m-80) REVERT: B 12 ASP cc_start: 0.9266 (t70) cc_final: 0.8765 (t0) REVERT: B 14 LEU cc_start: 0.9256 (mt) cc_final: 0.9047 (mt) REVERT: B 20 GLN cc_start: 0.8696 (mp10) cc_final: 0.7910 (mp10) REVERT: B 30 PHE cc_start: 0.9570 (m-80) cc_final: 0.9261 (m-80) REVERT: B 40 ARG cc_start: 0.9183 (mmp-170) cc_final: 0.8684 (mmm160) REVERT: B 42 LEU cc_start: 0.9811 (mt) cc_final: 0.9607 (mt) REVERT: B 120 ASN cc_start: 0.9459 (t0) cc_final: 0.9089 (t0) REVERT: B 151 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8736 (tm-30) REVERT: B 177 LYS cc_start: 0.8504 (mppt) cc_final: 0.8241 (mmtm) REVERT: B 213 LYS cc_start: 0.9582 (tptp) cc_final: 0.9378 (tppt) REVERT: B 217 GLU cc_start: 0.9461 (pt0) cc_final: 0.9188 (tm-30) REVERT: B 219 PHE cc_start: 0.9258 (m-80) cc_final: 0.9024 (m-80) REVERT: C 127 MET cc_start: 0.8377 (tmm) cc_final: 0.8087 (tmm) REVERT: C 264 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8910 (ptpp) REVERT: C 289 LYS cc_start: 0.9705 (mttt) cc_final: 0.9487 (mmtp) REVERT: C 306 TYR cc_start: 0.8493 (t80) cc_final: 0.7796 (t80) REVERT: C 396 MET cc_start: 0.9015 (tpt) cc_final: 0.7900 (tpt) REVERT: C 439 PHE cc_start: 0.9223 (t80) cc_final: 0.8657 (t80) REVERT: C 441 ASP cc_start: 0.9070 (m-30) cc_final: 0.8673 (m-30) REVERT: C 442 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8729 (tp40) REVERT: C 466 GLU cc_start: 0.9236 (pm20) cc_final: 0.8953 (pm20) REVERT: C 479 HIS cc_start: 0.9007 (m90) cc_final: 0.8760 (m-70) REVERT: C 482 ARG cc_start: 0.8956 (mtt90) cc_final: 0.7860 (mpt180) REVERT: C 483 MET cc_start: 0.8492 (tpp) cc_final: 0.7941 (tpp) REVERT: C 511 PHE cc_start: 0.8966 (m-80) cc_final: 0.8085 (m-10) REVERT: C 516 TYR cc_start: 0.9631 (m-80) cc_final: 0.9362 (m-80) REVERT: C 536 GLU cc_start: 0.8871 (pt0) cc_final: 0.8587 (pt0) REVERT: C 543 GLN cc_start: 0.7749 (tt0) cc_final: 0.7044 (tt0) REVERT: C 585 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8232 (tp40) REVERT: C 601 ASP cc_start: 0.9272 (t0) cc_final: 0.8783 (p0) REVERT: C 607 MET cc_start: 0.8516 (mtm) cc_final: 0.8311 (mtm) REVERT: C 613 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8658 (mtm-85) REVERT: C 620 ARG cc_start: 0.9327 (tpm170) cc_final: 0.8801 (tpm170) REVERT: C 713 MET cc_start: 0.8811 (tpp) cc_final: 0.8396 (ptp) REVERT: C 743 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8409 (mp0) REVERT: C 744 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8928 (mp0) REVERT: C 754 GLU cc_start: 0.8767 (pt0) cc_final: 0.8021 (pt0) REVERT: C 818 GLU cc_start: 0.9591 (tp30) cc_final: 0.9262 (tm-30) REVERT: C 846 LYS cc_start: 0.9171 (tptt) cc_final: 0.8751 (tppt) REVERT: C 892 LYS cc_start: 0.9219 (ptpt) cc_final: 0.8789 (ptpt) REVERT: C 904 MET cc_start: 0.9242 (tpp) cc_final: 0.8834 (tpp) REVERT: C 930 GLN cc_start: 0.9463 (pt0) cc_final: 0.9205 (pt0) REVERT: C 933 GLU cc_start: 0.8834 (tt0) cc_final: 0.8450 (tt0) REVERT: C 939 CYS cc_start: 0.9438 (m) cc_final: 0.9217 (m) REVERT: C 944 TRP cc_start: 0.8696 (p90) cc_final: 0.8136 (p90) REVERT: C 962 GLU cc_start: 0.8548 (mp0) cc_final: 0.8241 (mp0) REVERT: C 1021 TYR cc_start: 0.8313 (m-80) cc_final: 0.8082 (m-80) REVERT: C 1036 LEU cc_start: 0.9090 (mt) cc_final: 0.8741 (mt) REVERT: C 1039 ASP cc_start: 0.9328 (m-30) cc_final: 0.8879 (m-30) REVERT: C 1040 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7801 (mptt) REVERT: C 1051 MET cc_start: 0.9100 (tpp) cc_final: 0.8729 (mmm) REVERT: C 1071 MET cc_start: 0.7495 (pmm) cc_final: 0.6300 (pmm) REVERT: C 1076 MET cc_start: 0.9209 (mtp) cc_final: 0.8642 (ttm) REVERT: C 1077 GLN cc_start: 0.9467 (mt0) cc_final: 0.9083 (mt0) REVERT: C 1086 GLN cc_start: 0.9441 (pt0) cc_final: 0.9117 (pt0) REVERT: C 1090 THR cc_start: 0.9112 (m) cc_final: 0.8791 (p) REVERT: C 1091 ILE cc_start: 0.9123 (pt) cc_final: 0.8848 (pt) REVERT: C 1092 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8536 (mtpp) REVERT: C 1121 PHE cc_start: 0.9461 (t80) cc_final: 0.9239 (t80) REVERT: C 1124 LEU cc_start: 0.9595 (tt) cc_final: 0.9271 (tt) REVERT: C 1127 GLU cc_start: 0.9025 (pp20) cc_final: 0.8757 (pp20) REVERT: C 1128 LEU cc_start: 0.9457 (mt) cc_final: 0.9201 (mt) REVERT: D 29 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8887 (ptpp) REVERT: D 52 PHE cc_start: 0.8058 (m-80) cc_final: 0.6986 (m-10) REVERT: D 66 LYS cc_start: 0.9223 (ptpp) cc_final: 0.8904 (mmmt) REVERT: D 118 LEU cc_start: 0.9322 (mm) cc_final: 0.8858 (mm) REVERT: D 119 ASP cc_start: 0.8466 (t70) cc_final: 0.8111 (t0) REVERT: D 120 LEU cc_start: 0.8891 (mm) cc_final: 0.8374 (tp) REVERT: D 124 ASP cc_start: 0.9528 (m-30) cc_final: 0.9230 (m-30) REVERT: D 126 GLU cc_start: 0.9163 (pp20) cc_final: 0.8798 (pp20) REVERT: D 127 LYS cc_start: 0.9605 (mtmm) cc_final: 0.9297 (mttt) REVERT: D 205 MET cc_start: 0.9068 (mmm) cc_final: 0.8706 (mmp) REVERT: D 262 GLN cc_start: 0.9531 (tt0) cc_final: 0.9047 (tp-100) REVERT: D 341 ASN cc_start: 0.8881 (m-40) cc_final: 0.8446 (m110) REVERT: D 346 ARG cc_start: 0.9319 (ttm110) cc_final: 0.8410 (ptp-110) REVERT: D 356 ARG cc_start: 0.9475 (mtm180) cc_final: 0.9101 (mtm180) REVERT: D 364 GLU cc_start: 0.8818 (pp20) cc_final: 0.8599 (pp20) REVERT: D 386 ARG cc_start: 0.7940 (tpt170) cc_final: 0.7578 (mmm160) REVERT: D 397 ARG cc_start: 0.8676 (ptm-80) cc_final: 0.8270 (tmm-80) REVERT: D 427 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.7634 (ttm-80) REVERT: D 457 MET cc_start: 0.9530 (tmm) cc_final: 0.8978 (tpp) REVERT: D 475 MET cc_start: 0.8993 (mmp) cc_final: 0.8762 (mmp) REVERT: D 503 THR cc_start: 0.8328 (p) cc_final: 0.7672 (p) REVERT: D 505 HIS cc_start: 0.9152 (p-80) cc_final: 0.8767 (p-80) REVERT: D 510 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: D 515 MET cc_start: 0.8661 (mmp) cc_final: 0.8280 (mmm) REVERT: D 518 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6528 (mp0) REVERT: D 523 GLN cc_start: 0.8688 (tt0) cc_final: 0.8205 (tp40) REVERT: D 527 LEU cc_start: 0.9336 (mt) cc_final: 0.9036 (mt) REVERT: D 554 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8618 (mt-10) REVERT: D 560 LEU cc_start: 0.9509 (tp) cc_final: 0.9298 (tp) REVERT: D 563 ASN cc_start: 0.8985 (m-40) cc_final: 0.8665 (m-40) REVERT: D 576 MET cc_start: 0.9127 (ppp) cc_final: 0.8876 (ppp) REVERT: D 581 MET cc_start: 0.8905 (mtm) cc_final: 0.8519 (mtm) REVERT: D 637 LEU cc_start: 0.9187 (mm) cc_final: 0.8786 (mm) REVERT: D 641 ARG cc_start: 0.9179 (tpt-90) cc_final: 0.8869 (tpp80) REVERT: D 672 MET cc_start: 0.9384 (ttp) cc_final: 0.9163 (ttp) REVERT: D 706 MET cc_start: 0.8898 (ptm) cc_final: 0.8507 (pmm) REVERT: D 757 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8955 (tm-30) REVERT: D 780 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8367 (tt0) REVERT: D 784 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8946 (mm-30) REVERT: D 840 PHE cc_start: 0.9068 (m-80) cc_final: 0.8707 (m-80) REVERT: D 844 LEU cc_start: 0.8744 (mm) cc_final: 0.7867 (tp) REVERT: D 854 HIS cc_start: 0.9073 (m-70) cc_final: 0.8752 (m-70) REVERT: D 866 ARG cc_start: 0.9270 (ptt180) cc_final: 0.8709 (ptm160) REVERT: D 869 ASP cc_start: 0.9007 (t70) cc_final: 0.8600 (t0) REVERT: D 872 TYR cc_start: 0.8994 (t80) cc_final: 0.8591 (t80) REVERT: D 875 ARG cc_start: 0.9545 (mmm-85) cc_final: 0.9093 (mmm160) REVERT: D 917 GLU cc_start: 0.9136 (mp0) cc_final: 0.8782 (mp0) REVERT: D 928 ASP cc_start: 0.8726 (p0) cc_final: 0.8422 (p0) REVERT: D 962 VAL cc_start: 0.9286 (m) cc_final: 0.9024 (p) REVERT: D 1001 GLN cc_start: 0.9437 (tt0) cc_final: 0.8893 (tp-100) REVERT: D 1028 LEU cc_start: 0.9549 (tp) cc_final: 0.9271 (tp) REVERT: D 1139 GLN cc_start: 0.9255 (tp40) cc_final: 0.8885 (tp-100) REVERT: D 1151 ASP cc_start: 0.8556 (t0) cc_final: 0.8119 (t0) REVERT: D 1231 ARG cc_start: 0.9287 (ptt180) cc_final: 0.8997 (ptt-90) REVERT: E 43 LEU cc_start: 0.9623 (mm) cc_final: 0.9386 (mm) REVERT: E 46 ARG cc_start: 0.9194 (mmp80) cc_final: 0.8984 (mtt90) REVERT: E 50 LYS cc_start: 0.9526 (mtpt) cc_final: 0.9164 (mtpt) REVERT: E 59 LYS cc_start: 0.9289 (mtmm) cc_final: 0.8811 (ptmt) REVERT: E 65 ASN cc_start: 0.9109 (t0) cc_final: 0.8881 (t0) REVERT: E 66 ASP cc_start: 0.8804 (m-30) cc_final: 0.8490 (m-30) REVERT: E 97 ARG cc_start: 0.9512 (mtp-110) cc_final: 0.9226 (mtm110) REVERT: E 108 GLU cc_start: 0.9248 (pm20) cc_final: 0.7968 (tm-30) REVERT: F 213 ARG cc_start: 0.8682 (ppt170) cc_final: 0.8130 (ttp80) REVERT: F 252 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8723 (mmm160) REVERT: F 258 TYR cc_start: 0.9184 (t80) cc_final: 0.8873 (t80) REVERT: F 281 MET cc_start: 0.8857 (ppp) cc_final: 0.8589 (ppp) REVERT: F 282 MET cc_start: 0.9119 (pmm) cc_final: 0.8630 (pmm) REVERT: F 335 PHE cc_start: 0.9449 (t80) cc_final: 0.9177 (t80) REVERT: F 349 TRP cc_start: 0.7847 (m-10) cc_final: 0.7132 (t60) REVERT: F 352 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8452 (mtm180) REVERT: F 357 ARG cc_start: 0.9642 (tmt170) cc_final: 0.9319 (tpt90) REVERT: F 372 MET cc_start: 0.9554 (mmp) cc_final: 0.9327 (mmm) REVERT: F 501 GLU cc_start: 0.8717 (mp0) cc_final: 0.8366 (tp30) REVERT: J 84 MET cc_start: 0.9264 (mpp) cc_final: 0.9043 (mpp) REVERT: J 86 LEU cc_start: 0.9641 (tp) cc_final: 0.9333 (mt) REVERT: J 91 ILE cc_start: 0.8726 (pt) cc_final: 0.8420 (pt) REVERT: M 71 PHE cc_start: 0.9259 (m-10) cc_final: 0.8996 (m-80) REVERT: M 156 GLU cc_start: 0.9709 (tm-30) cc_final: 0.9421 (mm-30) outliers start: 3 outliers final: 1 residues processed: 909 average time/residue: 0.1959 time to fit residues: 278.8585 Evaluate side-chains 785 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 783 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 268 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 342 optimal weight: 4.9990 chunk 186 optimal weight: 0.0070 chunk 326 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 HIS C 986 GLN C1035 HIS D 233 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.109117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077839 restraints weight = 99237.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079699 restraints weight = 59665.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081183 restraints weight = 36638.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081582 restraints weight = 28291.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082616 restraints weight = 24260.117| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30158 Z= 0.172 Angle : 0.797 24.477 41380 Z= 0.413 Chirality : 0.055 1.918 4726 Planarity : 0.008 0.359 5007 Dihedral : 17.555 177.586 5172 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 0.03 % Allowed : 0.80 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3441 helix: 0.04 (0.14), residues: 1397 sheet: -0.70 (0.27), residues: 374 loop : -1.29 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 770 TYR 0.045 0.002 TYR D 25 PHE 0.035 0.002 PHE C 214 TRP 0.067 0.003 TRP M 112 HIS 0.007 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (30150) covalent geometry : angle 0.79096 / 0.41 (41368) hydrogen bonds : bond 0.04602 / 3.07 ( 1389) hydrogen bonds : angle 5.32661 / 3.77 ( 3855) metal coordination : bond 0.01228 / 0.41 ( 8) metal coordination : angle 5.59807 / 3.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 877 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8861 (ttp-170) cc_final: 0.8129 (ptm160) REVERT: A 30 PHE cc_start: 0.7653 (m-10) cc_final: 0.7349 (m-10) REVERT: A 34 LEU cc_start: 0.9406 (tp) cc_final: 0.9004 (tp) REVERT: A 83 LEU cc_start: 0.9660 (tp) cc_final: 0.9451 (mm) REVERT: A 125 ILE cc_start: 0.9588 (mm) cc_final: 0.9377 (mm) REVERT: A 138 LEU cc_start: 0.9346 (mp) cc_final: 0.9099 (mp) REVERT: A 151 GLN cc_start: 0.7977 (mp-120) cc_final: 0.7513 (pm20) REVERT: A 197 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8238 (mm-30) REVERT: A 208 LEU cc_start: 0.9585 (mm) cc_final: 0.9346 (mm) REVERT: A 219 PHE cc_start: 0.8103 (m-80) cc_final: 0.7618 (m-80) REVERT: B 12 ASP cc_start: 0.9287 (t70) cc_final: 0.8727 (t0) REVERT: B 20 GLN cc_start: 0.8609 (mp10) cc_final: 0.7815 (mp10) REVERT: B 30 PHE cc_start: 0.9519 (m-80) cc_final: 0.9243 (m-80) REVERT: B 40 ARG cc_start: 0.9112 (mmp-170) cc_final: 0.8621 (mmm160) REVERT: B 42 LEU cc_start: 0.9808 (mt) cc_final: 0.9605 (mt) REVERT: B 120 ASN cc_start: 0.9436 (t0) cc_final: 0.9050 (t0) REVERT: B 151 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8607 (tm-30) REVERT: B 177 LYS cc_start: 0.8495 (mppt) cc_final: 0.8294 (mmtm) REVERT: B 213 LYS cc_start: 0.9589 (tptp) cc_final: 0.9311 (tppt) REVERT: B 217 GLU cc_start: 0.9434 (pt0) cc_final: 0.9163 (tm-30) REVERT: B 219 PHE cc_start: 0.9264 (m-80) cc_final: 0.9026 (m-80) REVERT: C 127 MET cc_start: 0.8440 (tmm) cc_final: 0.8152 (tmm) REVERT: C 289 LYS cc_start: 0.9710 (mttt) cc_final: 0.9489 (mmtp) REVERT: C 306 TYR cc_start: 0.8353 (t80) cc_final: 0.7822 (t80) REVERT: C 308 LEU cc_start: 0.9503 (tp) cc_final: 0.9291 (tp) REVERT: C 355 MET cc_start: 0.8599 (tmm) cc_final: 0.8393 (ttm) REVERT: C 402 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9232 (tm-30) REVERT: C 404 MET cc_start: 0.9210 (tpt) cc_final: 0.9002 (tpt) REVERT: C 439 PHE cc_start: 0.9080 (t80) cc_final: 0.8389 (t80) REVERT: C 482 ARG cc_start: 0.8852 (mtt90) cc_final: 0.7673 (mmt90) REVERT: C 483 MET cc_start: 0.8523 (tpp) cc_final: 0.8058 (tpp) REVERT: C 511 PHE cc_start: 0.8992 (m-80) cc_final: 0.8106 (m-10) REVERT: C 543 GLN cc_start: 0.7766 (tt0) cc_final: 0.7560 (tm-30) REVERT: C 562 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8301 (mtm180) REVERT: C 585 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8335 (tp40) REVERT: C 601 ASP cc_start: 0.9212 (t0) cc_final: 0.8374 (p0) REVERT: C 604 ARG cc_start: 0.8541 (mmt-90) cc_final: 0.7742 (tpp-160) REVERT: C 613 ARG cc_start: 0.9281 (mtm110) cc_final: 0.8616 (mtm-85) REVERT: C 620 ARG cc_start: 0.9294 (tpm170) cc_final: 0.8771 (tpm170) REVERT: C 651 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 713 MET cc_start: 0.8775 (tpp) cc_final: 0.8450 (ptp) REVERT: C 744 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8902 (mp0) REVERT: C 818 GLU cc_start: 0.9601 (tp30) cc_final: 0.9251 (tm-30) REVERT: C 846 LYS cc_start: 0.9133 (tptt) cc_final: 0.8788 (tppt) REVERT: C 892 LYS cc_start: 0.9182 (ptpt) cc_final: 0.8728 (ptpt) REVERT: C 904 MET cc_start: 0.9241 (tpp) cc_final: 0.8825 (tpp) REVERT: C 926 MET cc_start: 0.8993 (tpt) cc_final: 0.8278 (tpt) REVERT: C 930 GLN cc_start: 0.9450 (pt0) cc_final: 0.9122 (pt0) REVERT: C 933 GLU cc_start: 0.8779 (tt0) cc_final: 0.8466 (tt0) REVERT: C 939 CYS cc_start: 0.9418 (m) cc_final: 0.9138 (m) REVERT: C 944 TRP cc_start: 0.8697 (p90) cc_final: 0.8146 (p90) REVERT: C 962 GLU cc_start: 0.8493 (mp0) cc_final: 0.8198 (mp0) REVERT: C 988 LEU cc_start: 0.9545 (mm) cc_final: 0.9185 (mm) REVERT: C 1021 TYR cc_start: 0.8320 (m-80) cc_final: 0.8069 (m-80) REVERT: C 1036 LEU cc_start: 0.9029 (mt) cc_final: 0.8715 (mt) REVERT: C 1039 ASP cc_start: 0.9323 (m-30) cc_final: 0.8911 (m-30) REVERT: C 1040 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7846 (mptt) REVERT: C 1051 MET cc_start: 0.9085 (tpp) cc_final: 0.8743 (mmm) REVERT: C 1071 MET cc_start: 0.7550 (pmm) cc_final: 0.6419 (pmm) REVERT: C 1076 MET cc_start: 0.9288 (mtp) cc_final: 0.8668 (ttm) REVERT: C 1077 GLN cc_start: 0.9509 (mt0) cc_final: 0.9109 (mt0) REVERT: C 1086 GLN cc_start: 0.9400 (pt0) cc_final: 0.9055 (pt0) REVERT: C 1090 THR cc_start: 0.9113 (m) cc_final: 0.8809 (p) REVERT: C 1092 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8366 (mtpp) REVERT: C 1121 PHE cc_start: 0.9446 (t80) cc_final: 0.9206 (t80) REVERT: C 1124 LEU cc_start: 0.9602 (tt) cc_final: 0.9332 (tt) REVERT: C 1127 GLU cc_start: 0.9001 (pp20) cc_final: 0.8792 (pp20) REVERT: C 1128 LEU cc_start: 0.9453 (mt) cc_final: 0.9176 (mt) REVERT: D 25 TYR cc_start: 0.9055 (m-80) cc_final: 0.8539 (m-80) REVERT: D 29 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8895 (ptpp) REVERT: D 66 LYS cc_start: 0.9251 (ptpp) cc_final: 0.8922 (mmmt) REVERT: D 118 LEU cc_start: 0.9328 (mm) cc_final: 0.9106 (mm) REVERT: D 124 ASP cc_start: 0.9530 (m-30) cc_final: 0.9125 (m-30) REVERT: D 126 GLU cc_start: 0.9154 (pp20) cc_final: 0.8752 (pp20) REVERT: D 127 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9246 (mttt) REVERT: D 256 MET cc_start: 0.7454 (tpp) cc_final: 0.7082 (tpp) REVERT: D 262 GLN cc_start: 0.9520 (tt0) cc_final: 0.8978 (tm-30) REVERT: D 275 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9283 (pt0) REVERT: D 341 ASN cc_start: 0.8931 (m-40) cc_final: 0.8462 (m-40) REVERT: D 346 ARG cc_start: 0.9329 (ttm110) cc_final: 0.8554 (ptp-110) REVERT: D 356 ARG cc_start: 0.9456 (mtm180) cc_final: 0.9077 (mtm180) REVERT: D 364 GLU cc_start: 0.8895 (pp20) cc_final: 0.8465 (tm-30) REVERT: D 386 ARG cc_start: 0.8007 (tpt170) cc_final: 0.7590 (mmm160) REVERT: D 397 ARG cc_start: 0.8682 (ptm-80) cc_final: 0.8260 (tmm-80) REVERT: D 424 TYR cc_start: 0.8836 (m-10) cc_final: 0.8414 (m-10) REVERT: D 427 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.7517 (ttm-80) REVERT: D 457 MET cc_start: 0.9490 (tmm) cc_final: 0.8877 (tpp) REVERT: D 475 MET cc_start: 0.8957 (mmp) cc_final: 0.8726 (mmp) REVERT: D 503 THR cc_start: 0.8421 (p) cc_final: 0.7795 (p) REVERT: D 505 HIS cc_start: 0.9133 (p-80) cc_final: 0.8768 (p-80) REVERT: D 515 MET cc_start: 0.8562 (mmp) cc_final: 0.8294 (mmm) REVERT: D 523 GLN cc_start: 0.8654 (tt0) cc_final: 0.8139 (tp40) REVERT: D 527 LEU cc_start: 0.9310 (mt) cc_final: 0.8998 (mt) REVERT: D 554 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8641 (mt-10) REVERT: D 560 LEU cc_start: 0.9520 (tp) cc_final: 0.9271 (tp) REVERT: D 563 ASN cc_start: 0.9007 (m-40) cc_final: 0.8684 (m-40) REVERT: D 576 MET cc_start: 0.9108 (ppp) cc_final: 0.8871 (ppp) REVERT: D 581 MET cc_start: 0.8928 (mtm) cc_final: 0.8555 (mtm) REVERT: D 636 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8245 (mmm160) REVERT: D 641 ARG cc_start: 0.9141 (tpt-90) cc_final: 0.8876 (tpp80) REVERT: D 706 MET cc_start: 0.8810 (ptm) cc_final: 0.8439 (pmm) REVERT: D 757 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8975 (tm-30) REVERT: D 780 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8402 (tt0) REVERT: D 784 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9010 (mm-30) REVERT: D 844 LEU cc_start: 0.8745 (mm) cc_final: 0.7800 (tp) REVERT: D 854 HIS cc_start: 0.9015 (m-70) cc_final: 0.8733 (m-70) REVERT: D 862 ASP cc_start: 0.9116 (t0) cc_final: 0.8894 (t0) REVERT: D 866 ARG cc_start: 0.9273 (ptt180) cc_final: 0.8755 (ptm160) REVERT: D 869 ASP cc_start: 0.9012 (t70) cc_final: 0.8581 (t0) REVERT: D 872 TYR cc_start: 0.8973 (t80) cc_final: 0.8498 (t80) REVERT: D 875 ARG cc_start: 0.9514 (mmm-85) cc_final: 0.9048 (mmm160) REVERT: D 928 ASP cc_start: 0.8687 (p0) cc_final: 0.8386 (p0) REVERT: D 962 VAL cc_start: 0.9322 (m) cc_final: 0.9025 (p) REVERT: D 983 MET cc_start: 0.8109 (tpp) cc_final: 0.7908 (tpt) REVERT: D 1001 GLN cc_start: 0.9481 (tt0) cc_final: 0.8965 (tp-100) REVERT: D 1028 LEU cc_start: 0.9557 (tp) cc_final: 0.9246 (tp) REVERT: D 1033 GLU cc_start: 0.9307 (tm-30) cc_final: 0.8753 (tm-30) REVERT: D 1038 ARG cc_start: 0.8293 (tmt170) cc_final: 0.7635 (ptm-80) REVERT: D 1112 MET cc_start: 0.8801 (tpt) cc_final: 0.8323 (tpp) REVERT: D 1139 GLN cc_start: 0.9217 (tp40) cc_final: 0.8918 (tp-100) REVERT: D 1140 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8982 (mt-10) REVERT: D 1151 ASP cc_start: 0.8576 (t0) cc_final: 0.8235 (t0) REVERT: D 1183 ARG cc_start: 0.9191 (ptp-110) cc_final: 0.8377 (ptp-170) REVERT: D 1231 ARG cc_start: 0.9304 (ptt180) cc_final: 0.9038 (ptt-90) REVERT: D 1244 LYS cc_start: 0.9273 (mmpt) cc_final: 0.8966 (tppt) REVERT: D 1267 TYR cc_start: 0.8594 (m-10) cc_final: 0.8117 (m-10) REVERT: E 43 LEU cc_start: 0.9630 (mm) cc_final: 0.9383 (mm) REVERT: E 50 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9194 (mtpt) REVERT: E 59 LYS cc_start: 0.9312 (mtmm) cc_final: 0.8795 (ptmt) REVERT: E 65 ASN cc_start: 0.9098 (t0) cc_final: 0.8814 (t0) REVERT: E 66 ASP cc_start: 0.8830 (m-30) cc_final: 0.8517 (m-30) REVERT: E 97 ARG cc_start: 0.9516 (mtp-110) cc_final: 0.9192 (mtm110) REVERT: F 213 ARG cc_start: 0.8696 (ppt170) cc_final: 0.8126 (ttp80) REVERT: F 252 ARG cc_start: 0.9157 (mtp85) cc_final: 0.8690 (mmm160) REVERT: F 258 TYR cc_start: 0.9208 (t80) cc_final: 0.8825 (t80) REVERT: F 281 MET cc_start: 0.9016 (ppp) cc_final: 0.8798 (ppp) REVERT: F 282 MET cc_start: 0.9156 (pmm) cc_final: 0.8663 (pmm) REVERT: F 333 GLU cc_start: 0.8441 (tt0) cc_final: 0.7895 (tm-30) REVERT: F 349 TRP cc_start: 0.7849 (m-10) cc_final: 0.7096 (t60) REVERT: F 352 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8446 (mtm180) REVERT: F 357 ARG cc_start: 0.9641 (tmt170) cc_final: 0.9318 (tpt90) REVERT: F 372 MET cc_start: 0.9542 (mmp) cc_final: 0.9325 (mmm) REVERT: F 377 ASN cc_start: 0.9654 (t0) cc_final: 0.8753 (t0) REVERT: F 501 GLU cc_start: 0.8672 (mp0) cc_final: 0.8323 (tp30) REVERT: J 81 HIS cc_start: 0.7607 (t70) cc_final: 0.7303 (t70) REVERT: J 86 LEU cc_start: 0.9645 (tp) cc_final: 0.9344 (mt) REVERT: M 71 PHE cc_start: 0.9264 (m-10) cc_final: 0.9007 (m-80) REVERT: M 156 GLU cc_start: 0.9704 (tm-30) cc_final: 0.9420 (mm-30) outliers start: 1 outliers final: 0 residues processed: 877 average time/residue: 0.1842 time to fit residues: 252.6159 Evaluate side-chains 770 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 770 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 203 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 335 optimal weight: 0.0050 chunk 287 optimal weight: 9.9990 chunk 191 optimal weight: 0.0980 chunk 233 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 GLN D 233 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 882 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN M 133 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077642 restraints weight = 98483.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080190 restraints weight = 52412.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081787 restraints weight = 32848.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082037 restraints weight = 26142.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082935 restraints weight = 24273.843| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 30158 Z= 0.163 Angle : 0.793 24.456 41380 Z= 0.413 Chirality : 0.055 1.922 4726 Planarity : 0.007 0.302 5007 Dihedral : 17.523 177.590 5172 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 0.07 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3441 helix: -0.02 (0.13), residues: 1394 sheet: -0.63 (0.27), residues: 368 loop : -1.27 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 562 TYR 0.023 0.002 TYR E 56 PHE 0.032 0.002 PHE C 214 TRP 0.072 0.003 TRP M 112 HIS 0.007 0.001 HIS C 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (30150) covalent geometry : angle 0.78912 / 0.41 (41368) hydrogen bonds : bond 0.04498 / 3.01 ( 1389) hydrogen bonds : angle 5.31298 / 3.76 ( 3855) metal coordination : bond 0.00954 / 0.31 ( 8) metal coordination : angle 4.91948 / 3.21 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 878 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8869 (ttp-170) cc_final: 0.8091 (ptm160) REVERT: A 30 PHE cc_start: 0.7583 (m-10) cc_final: 0.7292 (m-10) REVERT: A 34 LEU cc_start: 0.9402 (tp) cc_final: 0.9012 (tp) REVERT: A 38 LEU cc_start: 0.9766 (mt) cc_final: 0.9553 (mt) REVERT: A 83 LEU cc_start: 0.9663 (tp) cc_final: 0.9453 (mm) REVERT: A 125 ILE cc_start: 0.9571 (mm) cc_final: 0.9349 (mm) REVERT: A 138 LEU cc_start: 0.9372 (mp) cc_final: 0.9105 (mp) REVERT: A 151 GLN cc_start: 0.7941 (mp-120) cc_final: 0.7464 (pm20) REVERT: A 172 LEU cc_start: 0.9658 (mt) cc_final: 0.9433 (mt) REVERT: A 176 TYR cc_start: 0.8235 (p90) cc_final: 0.7994 (p90) REVERT: A 197 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8221 (mm-30) REVERT: A 219 PHE cc_start: 0.8028 (m-80) cc_final: 0.7540 (m-80) REVERT: B 12 ASP cc_start: 0.9304 (t70) cc_final: 0.8829 (t0) REVERT: B 20 GLN cc_start: 0.8634 (mp10) cc_final: 0.7884 (mp10) REVERT: B 30 PHE cc_start: 0.9524 (m-80) cc_final: 0.9250 (m-80) REVERT: B 40 ARG cc_start: 0.9165 (mmp-170) cc_final: 0.8648 (mmm160) REVERT: B 42 LEU cc_start: 0.9825 (mt) cc_final: 0.9615 (mt) REVERT: B 120 ASN cc_start: 0.9461 (t0) cc_final: 0.9080 (t0) REVERT: B 151 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8600 (tm-30) REVERT: B 213 LYS cc_start: 0.9576 (tptp) cc_final: 0.9316 (tppt) REVERT: B 217 GLU cc_start: 0.9385 (pt0) cc_final: 0.9165 (tm-30) REVERT: B 219 PHE cc_start: 0.9264 (m-80) cc_final: 0.9009 (m-80) REVERT: C 127 MET cc_start: 0.8465 (tmm) cc_final: 0.8160 (tmm) REVERT: C 213 GLU cc_start: 0.8702 (tp30) cc_final: 0.8397 (tp30) REVERT: C 289 LYS cc_start: 0.9706 (mttt) cc_final: 0.9476 (mmtp) REVERT: C 306 TYR cc_start: 0.8498 (t80) cc_final: 0.7944 (t80) REVERT: C 308 LEU cc_start: 0.9518 (tp) cc_final: 0.9307 (tp) REVERT: C 396 MET cc_start: 0.9054 (tpt) cc_final: 0.7924 (tpt) REVERT: C 402 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9244 (tm-30) REVERT: C 404 MET cc_start: 0.9219 (tpt) cc_final: 0.9011 (tpt) REVERT: C 439 PHE cc_start: 0.9010 (t80) cc_final: 0.8303 (t80) REVERT: C 482 ARG cc_start: 0.8793 (mtt90) cc_final: 0.7628 (mmt90) REVERT: C 483 MET cc_start: 0.8374 (tpp) cc_final: 0.7728 (tpp) REVERT: C 511 PHE cc_start: 0.8947 (m-80) cc_final: 0.8062 (m-10) REVERT: C 543 GLN cc_start: 0.7754 (tt0) cc_final: 0.7209 (tt0) REVERT: C 562 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7952 (mtm180) REVERT: C 585 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8184 (tp-100) REVERT: C 593 MET cc_start: 0.9198 (mmm) cc_final: 0.8941 (mmm) REVERT: C 611 MET cc_start: 0.8853 (ptt) cc_final: 0.8568 (ptt) REVERT: C 620 ARG cc_start: 0.9301 (tpm170) cc_final: 0.8956 (tpm170) REVERT: C 631 GLU cc_start: 0.8762 (pm20) cc_final: 0.8489 (mp0) REVERT: C 713 MET cc_start: 0.8745 (tpp) cc_final: 0.8383 (ptp) REVERT: C 754 GLU cc_start: 0.8836 (pt0) cc_final: 0.8221 (pt0) REVERT: C 818 GLU cc_start: 0.9634 (tp30) cc_final: 0.9277 (tm-30) REVERT: C 846 LYS cc_start: 0.9160 (tptt) cc_final: 0.8705 (tppt) REVERT: C 889 HIS cc_start: 0.7637 (m-70) cc_final: 0.6982 (m170) REVERT: C 892 LYS cc_start: 0.9144 (ptpt) cc_final: 0.8690 (ptpt) REVERT: C 904 MET cc_start: 0.9214 (tpp) cc_final: 0.8755 (tpp) REVERT: C 930 GLN cc_start: 0.9433 (pt0) cc_final: 0.9060 (pt0) REVERT: C 933 GLU cc_start: 0.8724 (tt0) cc_final: 0.8359 (tt0) REVERT: C 944 TRP cc_start: 0.8676 (p90) cc_final: 0.8347 (p90) REVERT: C 962 GLU cc_start: 0.8483 (mp0) cc_final: 0.8182 (mp0) REVERT: C 1021 TYR cc_start: 0.8337 (m-80) cc_final: 0.8074 (m-80) REVERT: C 1036 LEU cc_start: 0.9053 (mt) cc_final: 0.8664 (mt) REVERT: C 1039 ASP cc_start: 0.9308 (m-30) cc_final: 0.8878 (m-30) REVERT: C 1040 LYS cc_start: 0.8366 (mmtt) cc_final: 0.7770 (mptt) REVERT: C 1051 MET cc_start: 0.9097 (tpp) cc_final: 0.8748 (mmm) REVERT: C 1071 MET cc_start: 0.7570 (pmm) cc_final: 0.6580 (pmm) REVERT: C 1076 MET cc_start: 0.9249 (mtp) cc_final: 0.8683 (ttm) REVERT: C 1077 GLN cc_start: 0.9507 (mt0) cc_final: 0.9146 (mt0) REVERT: C 1086 GLN cc_start: 0.9379 (pt0) cc_final: 0.9032 (pt0) REVERT: C 1090 THR cc_start: 0.9140 (m) cc_final: 0.8859 (p) REVERT: C 1092 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8378 (mtpp) REVERT: C 1121 PHE cc_start: 0.9462 (t80) cc_final: 0.9224 (t80) REVERT: C 1127 GLU cc_start: 0.9012 (pp20) cc_final: 0.8804 (pp20) REVERT: C 1128 LEU cc_start: 0.9426 (mt) cc_final: 0.9212 (mt) REVERT: D 29 LYS cc_start: 0.9141 (ptpp) cc_final: 0.8831 (ptpp) REVERT: D 66 LYS cc_start: 0.9298 (ptpp) cc_final: 0.8985 (mmmt) REVERT: D 92 MET cc_start: 0.8061 (tpt) cc_final: 0.7366 (tpp) REVERT: D 118 LEU cc_start: 0.9337 (mm) cc_final: 0.9107 (mm) REVERT: D 124 ASP cc_start: 0.9539 (m-30) cc_final: 0.9179 (m-30) REVERT: D 126 GLU cc_start: 0.9151 (pp20) cc_final: 0.8752 (pp20) REVERT: D 127 LYS cc_start: 0.9599 (mtmm) cc_final: 0.9266 (mttt) REVERT: D 256 MET cc_start: 0.7476 (tpp) cc_final: 0.7058 (tpp) REVERT: D 262 GLN cc_start: 0.9526 (tt0) cc_final: 0.8983 (tm-30) REVERT: D 341 ASN cc_start: 0.8884 (m-40) cc_final: 0.8398 (m110) REVERT: D 346 ARG cc_start: 0.9353 (ttm110) cc_final: 0.8554 (ptp-110) REVERT: D 356 ARG cc_start: 0.9452 (mtm180) cc_final: 0.9070 (mtm180) REVERT: D 364 GLU cc_start: 0.8907 (pp20) cc_final: 0.8441 (tm-30) REVERT: D 368 ASN cc_start: 0.9547 (p0) cc_final: 0.9342 (p0) REVERT: D 379 ASP cc_start: 0.9433 (t0) cc_final: 0.9160 (t0) REVERT: D 386 ARG cc_start: 0.7941 (tpt170) cc_final: 0.7546 (mmm160) REVERT: D 397 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8245 (tmm-80) REVERT: D 427 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7463 (ttm-80) REVERT: D 457 MET cc_start: 0.9519 (tmm) cc_final: 0.8907 (tpp) REVERT: D 475 MET cc_start: 0.8990 (mmp) cc_final: 0.8742 (mmp) REVERT: D 503 THR cc_start: 0.8325 (p) cc_final: 0.7598 (p) REVERT: D 505 HIS cc_start: 0.9066 (p-80) cc_final: 0.8704 (p-80) REVERT: D 515 MET cc_start: 0.8564 (mmp) cc_final: 0.8310 (mmm) REVERT: D 523 GLN cc_start: 0.8657 (tt0) cc_final: 0.8102 (tp40) REVERT: D 527 LEU cc_start: 0.9319 (mt) cc_final: 0.9025 (mt) REVERT: D 541 MET cc_start: 0.8263 (tpt) cc_final: 0.8001 (tpp) REVERT: D 554 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8728 (mt-10) REVERT: D 560 LEU cc_start: 0.9510 (tp) cc_final: 0.9248 (tp) REVERT: D 563 ASN cc_start: 0.9052 (m-40) cc_final: 0.8739 (m-40) REVERT: D 574 LEU cc_start: 0.9066 (mt) cc_final: 0.8662 (mt) REVERT: D 576 MET cc_start: 0.9093 (ppp) cc_final: 0.8854 (ppp) REVERT: D 581 MET cc_start: 0.8947 (mtm) cc_final: 0.8575 (mtm) REVERT: D 641 ARG cc_start: 0.9121 (tpt-90) cc_final: 0.8842 (tpp80) REVERT: D 672 MET cc_start: 0.9330 (ttp) cc_final: 0.9123 (ttp) REVERT: D 698 ASN cc_start: 0.9421 (t0) cc_final: 0.9220 (t0) REVERT: D 706 MET cc_start: 0.8833 (ptm) cc_final: 0.8508 (pmm) REVERT: D 757 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8996 (tm-30) REVERT: D 780 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8363 (tt0) REVERT: D 784 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9007 (mm-30) REVERT: D 844 LEU cc_start: 0.8718 (mm) cc_final: 0.7770 (tp) REVERT: D 854 HIS cc_start: 0.9016 (m-70) cc_final: 0.8725 (m-70) REVERT: D 862 ASP cc_start: 0.9134 (t0) cc_final: 0.8911 (t0) REVERT: D 866 ARG cc_start: 0.9273 (ptt180) cc_final: 0.8710 (ptm160) REVERT: D 869 ASP cc_start: 0.8997 (t70) cc_final: 0.8576 (t0) REVERT: D 875 ARG cc_start: 0.9506 (mmm-85) cc_final: 0.9060 (mmm160) REVERT: D 917 GLU cc_start: 0.9203 (mp0) cc_final: 0.8862 (mp0) REVERT: D 928 ASP cc_start: 0.8785 (p0) cc_final: 0.8480 (p0) REVERT: D 983 MET cc_start: 0.8108 (tpp) cc_final: 0.7888 (tpt) REVERT: D 993 GLU cc_start: 0.8359 (mp0) cc_final: 0.7689 (mp0) REVERT: D 1001 GLN cc_start: 0.9489 (tt0) cc_final: 0.8954 (tp-100) REVERT: D 1028 LEU cc_start: 0.9558 (tp) cc_final: 0.9239 (tp) REVERT: D 1030 ARG cc_start: 0.9535 (tpt170) cc_final: 0.9331 (tpp80) REVERT: D 1033 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8785 (tm-30) REVERT: D 1038 ARG cc_start: 0.8266 (tmt170) cc_final: 0.7600 (ptm-80) REVERT: D 1112 MET cc_start: 0.8873 (tpt) cc_final: 0.8376 (tpp) REVERT: D 1139 GLN cc_start: 0.9238 (tp40) cc_final: 0.8952 (tp-100) REVERT: D 1140 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8975 (mt-10) REVERT: D 1151 ASP cc_start: 0.8645 (t0) cc_final: 0.8243 (t0) REVERT: D 1183 ARG cc_start: 0.9191 (ptp-110) cc_final: 0.8344 (ptp-170) REVERT: D 1231 ARG cc_start: 0.9327 (ptt180) cc_final: 0.9053 (ptt-90) REVERT: D 1244 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8983 (tppt) REVERT: D 1267 TYR cc_start: 0.8615 (m-10) cc_final: 0.8169 (m-10) REVERT: E 43 LEU cc_start: 0.9599 (mm) cc_final: 0.9346 (mm) REVERT: E 50 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9189 (mtpt) REVERT: E 59 LYS cc_start: 0.9330 (mtmm) cc_final: 0.8850 (ptmt) REVERT: E 65 ASN cc_start: 0.9190 (t0) cc_final: 0.8784 (t0) REVERT: E 66 ASP cc_start: 0.8829 (m-30) cc_final: 0.8488 (m-30) REVERT: E 90 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8608 (mtmt) REVERT: E 97 ARG cc_start: 0.9525 (mtp-110) cc_final: 0.9144 (mtm110) REVERT: E 108 GLU cc_start: 0.9321 (pm20) cc_final: 0.7918 (tm-30) REVERT: F 213 ARG cc_start: 0.8705 (ppt170) cc_final: 0.8148 (ttp80) REVERT: F 252 ARG cc_start: 0.9033 (mtp85) cc_final: 0.8695 (mmm160) REVERT: F 258 TYR cc_start: 0.9225 (t80) cc_final: 0.8917 (t80) REVERT: F 281 MET cc_start: 0.9030 (ppp) cc_final: 0.8816 (ppp) REVERT: F 282 MET cc_start: 0.9174 (pmm) cc_final: 0.8696 (pmm) REVERT: F 333 GLU cc_start: 0.8451 (tt0) cc_final: 0.7888 (tm-30) REVERT: F 349 TRP cc_start: 0.7819 (m-10) cc_final: 0.7064 (t60) REVERT: F 352 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8395 (mtm180) REVERT: F 357 ARG cc_start: 0.9648 (tmt170) cc_final: 0.9370 (tpt90) REVERT: F 372 MET cc_start: 0.9546 (mmp) cc_final: 0.9254 (mmm) REVERT: F 501 GLU cc_start: 0.8633 (mp0) cc_final: 0.8296 (tp30) REVERT: J 81 HIS cc_start: 0.7577 (t70) cc_final: 0.7275 (t70) REVERT: J 86 LEU cc_start: 0.9637 (tp) cc_final: 0.9325 (mt) REVERT: M 156 GLU cc_start: 0.9692 (tm-30) cc_final: 0.9434 (mm-30) outliers start: 2 outliers final: 1 residues processed: 878 average time/residue: 0.1883 time to fit residues: 260.0370 Evaluate side-chains 769 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 45 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 292 optimal weight: 5.9990 chunk 150 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 308 optimal weight: 30.0000 chunk 323 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.110457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080363 restraints weight = 98554.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081618 restraints weight = 60042.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083294 restraints weight = 36121.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083507 restraints weight = 28425.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084209 restraints weight = 25430.943| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30158 Z= 0.155 Angle : 0.799 24.461 41380 Z= 0.416 Chirality : 0.055 1.925 4726 Planarity : 0.007 0.289 5007 Dihedral : 17.464 177.603 5172 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 0.10 % Allowed : 0.35 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3441 helix: -0.07 (0.13), residues: 1395 sheet: -0.47 (0.28), residues: 342 loop : -1.30 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG D 350 TYR 0.029 0.002 TYR C 129 PHE 0.036 0.002 PHE C 214 TRP 0.067 0.002 TRP M 112 HIS 0.014 0.001 HIS C 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (30150) covalent geometry : angle 0.79559 / 0.42 (41368) hydrogen bonds : bond 0.04448 / 2.98 ( 1389) hydrogen bonds : angle 5.29744 / 3.75 ( 3855) metal coordination : bond 0.00852 / 0.28 ( 8) metal coordination : angle 4.57503 / 2.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6676.60 seconds wall clock time: 115 minutes 29.64 seconds (6929.64 seconds total)