Starting phenix.real_space_refine on Sun Jun 22 15:49:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.map" model { file = "/net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e74_27935/06_2025/8e74_27935.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.170 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 106 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 15861 2.51 5 N 4565 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25815 Number of models: 1 Model: "" Number of chains: 10 Chain: "Z" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8600 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1047} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9920 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "O" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 751 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 678 Classifications: {'RNA': 32} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 29} Chain breaks: 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 13556 SG CYS D 60 21.001 35.712 111.958 1.00 80.49 S ATOM 13574 SG CYS D 62 20.954 34.463 115.063 1.00 85.19 S ATOM 13683 SG CYS D 75 18.042 36.677 115.004 1.00 85.24 S ATOM 13709 SG CYS D 78 21.654 37.288 115.288 1.00 78.29 S ATOM 20124 SG CYS D 891 36.009 98.501 87.474 1.00 52.24 S ATOM 20691 SG CYS D 968 38.045 95.031 88.631 1.00 47.29 S ATOM 20733 SG CYS D 975 36.802 95.312 85.263 1.00 56.83 S ATOM 20751 SG CYS D 978 38.977 97.414 85.723 1.00 44.58 S Time building chain proxies: 15.40, per 1000 atoms: 0.60 Number of scatterers: 25815 At special positions: 0 Unit cell: (125.57, 128.817, 199.18, 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 88 16.00 P 106 15.00 Mg 1 11.99 O 5192 8.00 N 4565 7.00 C 15861 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: 6.93 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 42 sheets defined 39.7% alpha, 17.7% beta 43 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'Z' and resid 33 through 45 removed outlier: 3.850A pdb=" N SER Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS Z 45 " --> pdb=" O GLU Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 73 removed outlier: 4.044A pdb=" N GLN Z 71 " --> pdb=" O GLU Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 116 through 125 removed outlier: 3.848A pdb=" N ALA Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 151 Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.541A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.176A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.061A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.515A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.845A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.967A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (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 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.679A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.606A 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 288 through 301 removed outlier: 3.645A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.699A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.633A pdb=" N ILE C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.618A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.685A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.062A pdb=" N ALA C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.852A 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 removed outlier: 3.525A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.592A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.826A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.963A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 removed outlier: 3.535A pdb=" N ILE C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.749A 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 removed outlier: 3.506A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.613A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.290A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.954A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.750A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 187 removed outlier: 3.618A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.644A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.622A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.660A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.987A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.614A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.919A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.582A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.530A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.554A pdb=" N ARG D 459 " --> pdb=" O PHE D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.254A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (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 removed outlier: 3.583A pdb=" N ALA D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 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 726 removed outlier: 3.594A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.606A 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 819 removed outlier: 3.754A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.167A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.541A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.526A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.696A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.525A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.325A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.878A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.751A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.549A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'Z' and resid 79 through 83 removed outlier: 3.533A pdb=" N GLN Z 81 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL Z 51 " --> pdb=" O PHE Z 132 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE Z 132 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS Z 53 " --> pdb=" O THR Z 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 86 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 12 removed outlier: 5.844A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.601A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.635A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.330A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.540A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.451A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.071A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.294A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.455A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 215 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.179A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.548A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.414A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.667A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.703A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.724A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.518A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 784 through 785 removed outlier: 5.162A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.818A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD5, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD6, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.747A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.597A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.513A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 328 through 330 removed outlier: 3.659A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.391A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.956A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 6.262A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.785A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 1003 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 13.18 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7632 1.33 - 1.45: 3931 1.45 - 1.57: 14552 1.57 - 1.69: 208 1.69 - 1.81: 155 Bond restraints: 26478 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" CB ASP C 903 " pdb=" CG ASP C 903 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.38e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CA GLY C 608 " pdb=" C GLY C 608 " ideal model delta sigma weight residual 1.516 1.500 0.016 1.12e-02 7.97e+03 2.06e+00 ... (remaining 26473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 34933 1.46 - 2.92: 1198 2.92 - 4.39: 207 4.39 - 5.85: 7 5.85 - 7.31: 3 Bond angle restraints: 36348 Sorted by residual: angle pdb=" C PRO B 28 " pdb=" N GLY B 29 " pdb=" CA GLY B 29 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" N ILE B 159 " pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N VAL C 780 " pdb=" CA VAL C 780 " pdb=" C VAL C 780 " ideal model delta sigma weight residual 111.91 109.01 2.90 8.90e-01 1.26e+00 1.06e+01 angle pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 113.12 109.05 4.07 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N GLY D 508 " pdb=" CA GLY D 508 " pdb=" C GLY D 508 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.28e+00 ... (remaining 36343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 15294 34.30 - 68.59: 692 68.59 - 102.89: 38 102.89 - 137.19: 0 137.19 - 171.48: 5 Dihedral angle restraints: 16029 sinusoidal: 7309 harmonic: 8720 Sorted by residual: dihedral pdb=" CA ARG C 563 " pdb=" C ARG C 563 " pdb=" N LYS C 564 " pdb=" CA LYS C 564 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ALA C 766 " pdb=" C ALA C 766 " pdb=" N GLU C 767 " pdb=" CA GLU C 767 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DA P 118 " pdb=" C3' DA P 118 " pdb=" O3' DA P 118 " pdb=" P DA P 119 " ideal model delta sinusoidal sigma weight residual 220.00 48.52 171.48 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2710 0.034 - 0.069: 1011 0.069 - 0.103: 297 0.103 - 0.137: 147 0.137 - 0.172: 7 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE C1112 " pdb=" N ILE C1112 " pdb=" C ILE C1112 " pdb=" CB ILE C1112 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE D1149 " pdb=" N ILE D1149 " pdb=" C ILE D1149 " pdb=" CB ILE D1149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 4169 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 144 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C ARG D 144 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG D 144 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS D 145 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D 434 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO D 658 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " -0.024 5.00e-02 4.00e+02 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 30 2.31 - 2.96: 11987 2.96 - 3.61: 35937 3.61 - 4.25: 59233 4.25 - 4.90: 100247 Nonbonded interactions: 207434 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.665 2.170 nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 1.873 2.170 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 2.005 3.040 nonbonded pdb=" O ASP C 761 " pdb=" OG1 THR C 762 " model vdw 2.030 3.040 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.049 2.170 ... (remaining 207429 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 1 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 1 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 75.460 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.004 0.068 26486 Z= 0.202 Angle : 0.719 33.900 36360 Z= 0.391 Chirality : 0.043 0.172 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.975 171.483 10425 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 2.63 % Allowed : 9.89 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3032 helix: 0.19 (0.16), residues: 1107 sheet: -0.81 (0.26), residues: 416 loop : -1.44 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.005 0.001 HIS C 372 PHE 0.013 0.001 PHE C 906 TYR 0.016 0.001 TYR A 168 ARG 0.007 0.001 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.17975 ( 1087) hydrogen bonds : angle 6.70874 ( 3007) metal coordination : bond 0.03040 ( 8) metal coordination : angle 17.49555 ( 12) covalent geometry : bond 0.00440 (26478) covalent geometry : angle 0.64469 (36348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 125 ASN cc_start: 0.8532 (m-40) cc_final: 0.8288 (m-40) REVERT: A 137 GLU cc_start: 0.7885 (pp20) cc_final: 0.7664 (pp20) REVERT: B 177 LYS cc_start: 0.8144 (mttp) cc_final: 0.7801 (tttp) REVERT: C 336 GLU cc_start: 0.6677 (tp30) cc_final: 0.6427 (tp30) REVERT: C 393 MET cc_start: 0.8583 (mmt) cc_final: 0.8150 (mmt) REVERT: C 429 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6649 (tp30) REVERT: C 440 MET cc_start: 0.9028 (ttt) cc_final: 0.8612 (ttt) REVERT: C 529 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 733 ASP cc_start: 0.8435 (m-30) cc_final: 0.8139 (m-30) REVERT: C 758 ASP cc_start: 0.8160 (p0) cc_final: 0.7821 (p0) REVERT: C 760 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7362 (mtt90) REVERT: C 814 LEU cc_start: 0.1939 (OUTLIER) cc_final: 0.1247 (mm) REVERT: C 903 ASP cc_start: 0.8538 (p0) cc_final: 0.8333 (p0) REVERT: C 947 ASP cc_start: 0.7765 (p0) cc_final: 0.7315 (p0) REVERT: D 123 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8043 (mptp) REVERT: D 177 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.3691 (mp) REVERT: D 530 GLU cc_start: 0.7613 (tt0) cc_final: 0.7215 (pm20) REVERT: D 733 MET cc_start: 0.8912 (ptt) cc_final: 0.8640 (ptm) REVERT: D 796 ASP cc_start: 0.8282 (p0) cc_final: 0.8025 (p0) REVERT: D 1265 ASN cc_start: 0.8485 (m-40) cc_final: 0.8094 (m-40) outliers start: 67 outliers final: 31 residues processed: 357 average time/residue: 1.4902 time to fit residues: 620.8917 Evaluate side-chains 295 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 136 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 0.1980 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.0370 chunk 283 optimal weight: 0.9980 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 53 HIS A 100 GLN B 5 GLN B 79 ASN C 476 HIS C 603 ASN D 5 ASN D 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121213 restraints weight = 26304.039| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.76 r_work: 0.3153 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26486 Z= 0.145 Angle : 0.598 10.442 36360 Z= 0.316 Chirality : 0.043 0.182 4172 Planarity : 0.005 0.041 4401 Dihedral : 17.127 179.960 4702 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.39 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 12.32 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3032 helix: 0.80 (0.16), residues: 1096 sheet: -0.35 (0.25), residues: 422 loop : -1.28 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 223 HIS 0.004 0.001 HIS C 200 PHE 0.012 0.001 PHE C 153 TYR 0.014 0.001 TYR A 168 ARG 0.008 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.05360 ( 1087) hydrogen bonds : angle 4.84556 ( 3007) metal coordination : bond 0.00705 ( 8) metal coordination : angle 3.96481 ( 12) covalent geometry : bond 0.00326 (26478) covalent geometry : angle 0.59385 (36348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 306 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6391 (pp20) REVERT: Z 125 ASN cc_start: 0.8569 (m-40) cc_final: 0.8287 (m-40) REVERT: A 137 GLU cc_start: 0.8121 (pp20) cc_final: 0.7820 (pp20) REVERT: B 2 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7818 (mm) REVERT: B 52 THR cc_start: 0.8590 (m) cc_final: 0.8379 (p) REVERT: B 188 ASP cc_start: 0.8368 (t0) cc_final: 0.8095 (t0) REVERT: B 224 GLU cc_start: 0.7156 (pp20) cc_final: 0.6840 (pp20) REVERT: C 172 GLU cc_start: 0.8528 (tt0) cc_final: 0.8309 (tt0) REVERT: C 336 GLU cc_start: 0.6802 (tp30) cc_final: 0.6513 (tp30) REVERT: C 393 MET cc_start: 0.8714 (mmt) cc_final: 0.8370 (mmt) REVERT: C 429 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6711 (tp30) REVERT: C 467 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6965 (mpt-90) REVERT: C 584 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6932 (ptp-110) REVERT: C 733 ASP cc_start: 0.8507 (m-30) cc_final: 0.8199 (m-30) REVERT: C 758 ASP cc_start: 0.8558 (p0) cc_final: 0.8254 (p0) REVERT: C 814 LEU cc_start: 0.1002 (OUTLIER) cc_final: 0.0551 (mm) REVERT: C 843 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 853 PHE cc_start: 0.8117 (m-80) cc_final: 0.7858 (m-80) REVERT: C 947 ASP cc_start: 0.7783 (p0) cc_final: 0.7411 (p0) REVERT: D 177 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.3775 (mp) REVERT: D 215 GLU cc_start: 0.6352 (mp0) cc_final: 0.6108 (mp0) REVERT: D 541 MET cc_start: 0.9114 (mtm) cc_final: 0.8827 (mtm) REVERT: D 733 MET cc_start: 0.8818 (ptt) cc_final: 0.8601 (ptm) REVERT: D 744 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6938 (mt-10) REVERT: D 796 ASP cc_start: 0.8123 (p0) cc_final: 0.7912 (p0) REVERT: D 1265 ASN cc_start: 0.8332 (m-40) cc_final: 0.7890 (m110) REVERT: E 36 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8446 (p) outliers start: 77 outliers final: 46 residues processed: 360 average time/residue: 1.4508 time to fit residues: 605.6980 Evaluate side-chains 312 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 261 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 407 GLN C 603 ASN C1066 GLN D 239 ASN D1125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122842 restraints weight = 26051.290| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.79 r_work: 0.3167 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26486 Z= 0.120 Angle : 0.544 9.042 36360 Z= 0.290 Chirality : 0.042 0.170 4172 Planarity : 0.004 0.044 4401 Dihedral : 16.914 179.371 4690 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.99 % Favored : 95.68 % Rotamer: Outliers : 3.84 % Allowed : 13.10 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3032 helix: 1.20 (0.16), residues: 1080 sheet: -0.21 (0.25), residues: 419 loop : -1.16 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.003 0.001 HIS C1042 PHE 0.021 0.001 PHE D 6 TYR 0.012 0.001 TYR A 168 ARG 0.005 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1087) hydrogen bonds : angle 4.46861 ( 3007) metal coordination : bond 0.00444 ( 8) metal coordination : angle 2.94395 ( 12) covalent geometry : bond 0.00262 (26478) covalent geometry : angle 0.54188 (36348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 299 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6397 (pp20) REVERT: A 84 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8538 (t) REVERT: A 89 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: A 137 GLU cc_start: 0.8133 (pp20) cc_final: 0.7814 (pp20) REVERT: B 188 ASP cc_start: 0.8365 (t0) cc_final: 0.8109 (t0) REVERT: B 224 GLU cc_start: 0.7152 (pp20) cc_final: 0.6732 (pp20) REVERT: C 114 ASP cc_start: 0.8495 (m-30) cc_final: 0.8125 (m-30) REVERT: C 252 PHE cc_start: 0.8269 (m-80) cc_final: 0.7973 (m-80) REVERT: C 259 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6819 (mpp80) REVERT: C 336 GLU cc_start: 0.6744 (tp30) cc_final: 0.6452 (tp30) REVERT: C 393 MET cc_start: 0.8715 (mmt) cc_final: 0.8351 (mmt) REVERT: C 429 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6753 (tp30) REVERT: C 467 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6878 (mpt-90) REVERT: C 534 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: C 584 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6875 (ptp-110) REVERT: C 758 ASP cc_start: 0.8510 (p0) cc_final: 0.8254 (p0) REVERT: C 814 LEU cc_start: 0.0825 (OUTLIER) cc_final: 0.0440 (mm) REVERT: C 843 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 853 PHE cc_start: 0.8102 (m-80) cc_final: 0.7899 (m-80) REVERT: C 947 ASP cc_start: 0.7659 (p0) cc_final: 0.7345 (p0) REVERT: C 1063 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: D 123 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7907 (mmtm) REVERT: D 177 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.3788 (mp) REVERT: D 215 GLU cc_start: 0.6393 (mp0) cc_final: 0.6179 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6770 (OUTLIER) cc_final: 0.6425 (m) REVERT: D 250 GLU cc_start: 0.6951 (tp30) cc_final: 0.6703 (mm-30) REVERT: D 339 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7322 (t0) REVERT: D 356 ARG cc_start: 0.7630 (ttt90) cc_final: 0.6778 (ttp-110) REVERT: D 541 MET cc_start: 0.9078 (mtm) cc_final: 0.8852 (mtm) REVERT: D 791 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: D 796 ASP cc_start: 0.8049 (p0) cc_final: 0.7746 (p0) REVERT: D 1117 ASP cc_start: 0.7781 (p0) cc_final: 0.7517 (p0) REVERT: D 1250 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: D 1265 ASN cc_start: 0.8289 (m-40) cc_final: 0.7852 (m110) REVERT: E 66 ASP cc_start: 0.7853 (m-30) cc_final: 0.7354 (m-30) outliers start: 98 outliers final: 46 residues processed: 372 average time/residue: 1.3382 time to fit residues: 579.2555 Evaluate side-chains 331 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1250 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 0.0000 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 545 ASN C 603 ASN C1066 GLN D 239 ASN E 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119316 restraints weight = 26243.038| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.81 r_work: 0.3118 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26486 Z= 0.180 Angle : 0.595 12.227 36360 Z= 0.313 Chirality : 0.044 0.234 4172 Planarity : 0.005 0.047 4401 Dihedral : 16.905 179.209 4682 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.45 % Favored : 95.28 % Rotamer: Outliers : 4.28 % Allowed : 13.89 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3032 helix: 1.11 (0.16), residues: 1091 sheet: -0.24 (0.25), residues: 433 loop : -1.15 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 938 HIS 0.005 0.001 HIS C 479 PHE 0.021 0.002 PHE D 70 TYR 0.018 0.001 TYR A 168 ARG 0.007 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 1087) hydrogen bonds : angle 4.47256 ( 3007) metal coordination : bond 0.00473 ( 8) metal coordination : angle 2.75789 ( 12) covalent geometry : bond 0.00439 (26478) covalent geometry : angle 0.59283 (36348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 278 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8107 (pp20) cc_final: 0.7761 (pp20) REVERT: B 2 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7847 (mm) REVERT: B 34 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8183 (pt) REVERT: B 177 LYS cc_start: 0.8070 (mttp) cc_final: 0.7585 (tttp) REVERT: B 188 ASP cc_start: 0.8432 (t0) cc_final: 0.8085 (t0) REVERT: B 190 ASP cc_start: 0.8918 (m-30) cc_final: 0.8712 (m-30) REVERT: B 224 GLU cc_start: 0.7261 (pp20) cc_final: 0.6837 (pp20) REVERT: C 114 ASP cc_start: 0.8513 (m-30) cc_final: 0.8135 (m-30) REVERT: C 121 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7531 (mp0) REVERT: C 252 PHE cc_start: 0.8368 (m-80) cc_final: 0.8162 (m-80) REVERT: C 393 MET cc_start: 0.8680 (mmt) cc_final: 0.8305 (mmt) REVERT: C 429 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6764 (tp30) REVERT: C 584 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6970 (ptp-110) REVERT: C 758 ASP cc_start: 0.8456 (p0) cc_final: 0.8192 (p0) REVERT: C 814 LEU cc_start: 0.0988 (OUTLIER) cc_final: 0.0640 (mm) REVERT: C 843 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 885 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8795 (mt) REVERT: C 947 ASP cc_start: 0.7618 (p0) cc_final: 0.7287 (p0) REVERT: C 982 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: C 1063 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: D 39 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7266 (mp) REVERT: D 123 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7923 (mmtm) REVERT: D 177 LEU cc_start: 0.4455 (OUTLIER) cc_final: 0.3693 (mp) REVERT: D 215 GLU cc_start: 0.6434 (mp0) cc_final: 0.6220 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6836 (OUTLIER) cc_final: 0.6516 (m) REVERT: D 339 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (t0) REVERT: D 356 ARG cc_start: 0.7674 (ttt90) cc_final: 0.6513 (ttp-110) REVERT: D 744 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6993 (mp0) REVERT: D 796 ASP cc_start: 0.7986 (p0) cc_final: 0.7700 (p0) REVERT: D 1076 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7648 (p) REVERT: D 1112 MET cc_start: 0.7855 (mmm) cc_final: 0.7575 (mtp) REVERT: D 1117 ASP cc_start: 0.7840 (p0) cc_final: 0.7615 (p0) REVERT: D 1250 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: D 1265 ASN cc_start: 0.8317 (m-40) cc_final: 0.7868 (m110) REVERT: E 70 GLN cc_start: 0.4885 (OUTLIER) cc_final: 0.4148 (tm-30) outliers start: 109 outliers final: 62 residues processed: 361 average time/residue: 1.4047 time to fit residues: 585.9143 Evaluate side-chains 341 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 137 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 603 ASN C1066 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116943 restraints weight = 26258.310| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.77 r_work: 0.3095 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26486 Z= 0.217 Angle : 0.628 11.467 36360 Z= 0.330 Chirality : 0.045 0.173 4172 Planarity : 0.005 0.049 4401 Dihedral : 16.946 178.981 4677 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.68 % Favored : 95.12 % Rotamer: Outliers : 4.43 % Allowed : 15.34 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3032 helix: 0.97 (0.16), residues: 1097 sheet: -0.35 (0.25), residues: 438 loop : -1.19 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 938 HIS 0.007 0.001 HIS C 479 PHE 0.024 0.002 PHE D 70 TYR 0.021 0.002 TYR A 168 ARG 0.007 0.001 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 1087) hydrogen bonds : angle 4.51789 ( 3007) metal coordination : bond 0.00454 ( 8) metal coordination : angle 2.71668 ( 12) covalent geometry : bond 0.00538 (26478) covalent geometry : angle 0.62604 (36348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 276 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5908 (pp20) REVERT: Z 102 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6762 (ttp-110) REVERT: A 137 GLU cc_start: 0.8101 (pp20) cc_final: 0.7773 (pp20) REVERT: B 34 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8163 (pt) REVERT: B 177 LYS cc_start: 0.8105 (mttp) cc_final: 0.7641 (ttpp) REVERT: B 188 ASP cc_start: 0.8439 (t0) cc_final: 0.8074 (t0) REVERT: B 224 GLU cc_start: 0.7331 (pp20) cc_final: 0.7017 (pp20) REVERT: C 121 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7465 (mp0) REVERT: C 408 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: C 429 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6821 (tp30) REVERT: C 467 ARG cc_start: 0.7409 (mpt-90) cc_final: 0.6728 (mpt-90) REVERT: C 584 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6978 (ptp-110) REVERT: C 620 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (ttp80) REVERT: C 758 ASP cc_start: 0.8540 (p0) cc_final: 0.8246 (p0) REVERT: C 843 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 885 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8810 (mt) REVERT: C 947 ASP cc_start: 0.7699 (p0) cc_final: 0.7343 (p0) REVERT: C 982 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: C 1063 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: D 39 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7393 (mp) REVERT: D 123 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7915 (mmtm) REVERT: D 177 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.3625 (mm) REVERT: D 215 GLU cc_start: 0.6338 (mp0) cc_final: 0.6122 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6973 (OUTLIER) cc_final: 0.6644 (m) REVERT: D 243 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7530 (mt-10) REVERT: D 339 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7356 (t0) REVERT: D 356 ARG cc_start: 0.7601 (ttt90) cc_final: 0.6813 (ttp-110) REVERT: D 796 ASP cc_start: 0.7936 (p0) cc_final: 0.7653 (p0) REVERT: D 939 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 1076 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7681 (p) REVERT: D 1112 MET cc_start: 0.7960 (mmm) cc_final: 0.7603 (mtp) REVERT: D 1113 GLU cc_start: 0.7646 (tt0) cc_final: 0.7269 (tp30) REVERT: D 1117 ASP cc_start: 0.7900 (p0) cc_final: 0.7598 (p0) REVERT: D 1137 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: D 1265 ASN cc_start: 0.8341 (m-40) cc_final: 0.7903 (m110) REVERT: E 70 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4196 (tm-30) outliers start: 113 outliers final: 64 residues processed: 362 average time/residue: 1.3794 time to fit residues: 579.7019 Evaluate side-chains 344 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 265 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 225 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 308 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 603 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121447 restraints weight = 26180.097| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.74 r_work: 0.3159 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26486 Z= 0.116 Angle : 0.535 9.976 36360 Z= 0.285 Chirality : 0.042 0.179 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.751 178.499 4671 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 3.65 % Allowed : 16.63 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3032 helix: 1.27 (0.16), residues: 1094 sheet: -0.00 (0.25), residues: 418 loop : -1.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 723 HIS 0.002 0.001 HIS D 94 PHE 0.023 0.001 PHE D 70 TYR 0.011 0.001 TYR A 168 ARG 0.006 0.000 ARG Z 124 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 1087) hydrogen bonds : angle 4.26491 ( 3007) metal coordination : bond 0.00332 ( 8) metal coordination : angle 2.38674 ( 12) covalent geometry : bond 0.00258 (26478) covalent geometry : angle 0.53377 (36348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 300 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 137 GLU cc_start: 0.8099 (pp20) cc_final: 0.7779 (pp20) REVERT: B 188 ASP cc_start: 0.8371 (t0) cc_final: 0.8032 (t0) REVERT: B 224 GLU cc_start: 0.7231 (pp20) cc_final: 0.6827 (pp20) REVERT: C 121 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7376 (mp0) REVERT: C 393 MET cc_start: 0.8600 (mmt) cc_final: 0.8215 (mmt) REVERT: C 429 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6677 (tp30) REVERT: C 467 ARG cc_start: 0.7157 (mpt-90) cc_final: 0.6608 (mpt-90) REVERT: C 534 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: C 584 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6729 (ptp-110) REVERT: C 620 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: C 645 GLU cc_start: 0.8330 (tt0) cc_final: 0.7932 (mt-10) REVERT: C 758 ASP cc_start: 0.8512 (p0) cc_final: 0.8225 (p0) REVERT: C 760 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: C 761 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: C 843 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 947 ASP cc_start: 0.7624 (p0) cc_final: 0.7294 (p0) REVERT: C 1063 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 1066 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8799 (mm110) REVERT: D 35 ASN cc_start: 0.7646 (t0) cc_final: 0.7230 (t0) REVERT: D 39 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7432 (mp) REVERT: D 123 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7691 (mmtm) REVERT: D 215 GLU cc_start: 0.6346 (mp0) cc_final: 0.6138 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6539 (m) REVERT: D 238 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7218 (pm20) REVERT: D 248 TYR cc_start: 0.7196 (m-80) cc_final: 0.6995 (m-80) REVERT: D 250 GLU cc_start: 0.7135 (tp30) cc_final: 0.6703 (mm-30) REVERT: D 356 ARG cc_start: 0.7660 (ttt90) cc_final: 0.6600 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (p) REVERT: D 1112 MET cc_start: 0.7792 (mmm) cc_final: 0.7184 (mtp) REVERT: D 1113 GLU cc_start: 0.7723 (tt0) cc_final: 0.7262 (tp30) REVERT: D 1117 ASP cc_start: 0.7713 (p0) cc_final: 0.7398 (p0) REVERT: D 1137 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: D 1265 ASN cc_start: 0.8222 (m-40) cc_final: 0.7787 (m-40) REVERT: E 66 ASP cc_start: 0.7770 (m-30) cc_final: 0.7273 (m-30) outliers start: 93 outliers final: 44 residues processed: 369 average time/residue: 1.4265 time to fit residues: 610.6064 Evaluate side-chains 330 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1066 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.0030 chunk 293 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 188 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN C 545 ASN C 775 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121303 restraints weight = 26299.060| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.75 r_work: 0.3160 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26486 Z= 0.114 Angle : 0.528 9.845 36360 Z= 0.280 Chirality : 0.041 0.180 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.684 177.979 4669 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 3.14 % Allowed : 17.30 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3032 helix: 1.41 (0.16), residues: 1094 sheet: -0.01 (0.26), residues: 417 loop : -0.96 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.002 0.001 HIS D 94 PHE 0.025 0.001 PHE D 70 TYR 0.011 0.001 TYR A 168 ARG 0.008 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1087) hydrogen bonds : angle 4.17591 ( 3007) metal coordination : bond 0.00318 ( 8) metal coordination : angle 2.27264 ( 12) covalent geometry : bond 0.00255 (26478) covalent geometry : angle 0.52646 (36348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 288 time to evaluate : 3.019 Fit side-chains revert: symmetry clash REVERT: Z 113 MET cc_start: 0.9125 (ptt) cc_final: 0.8818 (ptt) REVERT: A 84 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 137 GLU cc_start: 0.8102 (pp20) cc_final: 0.7738 (pp20) REVERT: B 2 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7906 (mm) REVERT: B 224 GLU cc_start: 0.7195 (pp20) cc_final: 0.6808 (pp20) REVERT: C 121 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7363 (mp0) REVERT: C 429 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6716 (tp30) REVERT: C 467 ARG cc_start: 0.7037 (mpt-90) cc_final: 0.6545 (mpt-90) REVERT: C 534 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: C 584 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6737 (ptp-110) REVERT: C 645 GLU cc_start: 0.8323 (tt0) cc_final: 0.7963 (mt-10) REVERT: C 758 ASP cc_start: 0.8514 (p0) cc_final: 0.8203 (p0) REVERT: C 760 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7106 (mtp180) REVERT: C 761 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: C 843 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 885 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8773 (mt) REVERT: C 947 ASP cc_start: 0.7637 (p0) cc_final: 0.7299 (p0) REVERT: C 982 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 35 ASN cc_start: 0.7617 (t0) cc_final: 0.7194 (t0) REVERT: D 39 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7452 (mp) REVERT: D 123 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7734 (mmtm) REVERT: D 236 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6473 (m) REVERT: D 238 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7302 (tm-30) REVERT: D 248 TYR cc_start: 0.7334 (m-80) cc_final: 0.7085 (m-80) REVERT: D 356 ARG cc_start: 0.7604 (ttt90) cc_final: 0.6762 (ttp-110) REVERT: D 657 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7621 (tp40) REVERT: D 791 GLU cc_start: 0.7472 (tt0) cc_final: 0.7245 (tm-30) REVERT: D 1076 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7708 (p) REVERT: D 1087 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6590 (mtp85) REVERT: D 1112 MET cc_start: 0.7618 (mmm) cc_final: 0.7382 (mtp) REVERT: D 1117 ASP cc_start: 0.7718 (p0) cc_final: 0.7383 (p0) REVERT: D 1137 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: D 1265 ASN cc_start: 0.8198 (m-40) cc_final: 0.7758 (m-40) REVERT: E 66 ASP cc_start: 0.7733 (m-30) cc_final: 0.7266 (m-30) outliers start: 80 outliers final: 45 residues processed: 349 average time/residue: 1.4219 time to fit residues: 577.4683 Evaluate side-chains 334 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 300 optimal weight: 0.4980 chunk 256 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 212 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 GLN B 200 ASN C 232 GLN C 415 GLN C1066 GLN D 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122350 restraints weight = 26223.083| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.79 r_work: 0.3169 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26486 Z= 0.114 Angle : 0.538 14.100 36360 Z= 0.284 Chirality : 0.041 0.175 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.645 177.696 4669 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 3.18 % Allowed : 17.65 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3032 helix: 1.48 (0.16), residues: 1095 sheet: 0.05 (0.26), residues: 417 loop : -0.91 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.002 0.001 HIS D 94 PHE 0.027 0.001 PHE D 70 TYR 0.012 0.001 TYR E 67 ARG 0.008 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1087) hydrogen bonds : angle 4.13182 ( 3007) metal coordination : bond 0.00311 ( 8) metal coordination : angle 2.12608 ( 12) covalent geometry : bond 0.00254 (26478) covalent geometry : angle 0.53718 (36348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 292 time to evaluate : 2.944 Fit side-chains revert: symmetry clash REVERT: Z 113 MET cc_start: 0.9161 (ptt) cc_final: 0.8858 (ptt) REVERT: A 84 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 137 GLU cc_start: 0.8107 (pp20) cc_final: 0.7782 (pp20) REVERT: B 2 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 177 LYS cc_start: 0.8030 (mttp) cc_final: 0.7623 (tttp) REVERT: B 224 GLU cc_start: 0.7285 (pp20) cc_final: 0.6871 (pp20) REVERT: C 121 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7312 (mp0) REVERT: C 252 PHE cc_start: 0.8366 (m-80) cc_final: 0.8158 (m-80) REVERT: C 303 GLU cc_start: 0.7161 (pm20) cc_final: 0.6033 (tp30) REVERT: C 429 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6814 (tp30) REVERT: C 467 ARG cc_start: 0.7038 (mpt-90) cc_final: 0.6610 (mpt-90) REVERT: C 534 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: C 535 GLU cc_start: 0.8116 (mp0) cc_final: 0.7815 (mp0) REVERT: C 584 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6818 (ptp-110) REVERT: C 645 GLU cc_start: 0.8386 (tt0) cc_final: 0.8085 (mt-10) REVERT: C 697 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: C 758 ASP cc_start: 0.8526 (p0) cc_final: 0.8222 (p0) REVERT: C 760 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7126 (mtp180) REVERT: C 843 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 885 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 947 ASP cc_start: 0.7528 (p0) cc_final: 0.7161 (p0) REVERT: C 982 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 1051 MET cc_start: 0.8536 (ttm) cc_final: 0.8318 (mtp) REVERT: D 35 ASN cc_start: 0.7682 (t0) cc_final: 0.7268 (t0) REVERT: D 39 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7517 (mp) REVERT: D 123 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7841 (mmtm) REVERT: D 177 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3489 (mm) REVERT: D 215 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: D 236 VAL cc_start: 0.6816 (OUTLIER) cc_final: 0.6484 (m) REVERT: D 238 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7145 (tm-30) REVERT: D 248 TYR cc_start: 0.7375 (m-80) cc_final: 0.7126 (m-80) REVERT: D 250 GLU cc_start: 0.7061 (tp30) cc_final: 0.6655 (mm-30) REVERT: D 285 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5706 (ptpp) REVERT: D 356 ARG cc_start: 0.7735 (ttt90) cc_final: 0.6781 (ttp-110) REVERT: D 657 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: D 1076 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7693 (p) REVERT: D 1087 ARG cc_start: 0.7059 (mmm-85) cc_final: 0.6768 (mtp85) REVERT: D 1112 MET cc_start: 0.7737 (mmm) cc_final: 0.7452 (mtp) REVERT: D 1113 GLU cc_start: 0.7750 (tt0) cc_final: 0.7344 (tp30) REVERT: D 1117 ASP cc_start: 0.7772 (p0) cc_final: 0.7448 (p0) REVERT: D 1137 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: D 1265 ASN cc_start: 0.8211 (m-40) cc_final: 0.7793 (m-40) REVERT: E 66 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7349 (m-30) outliers start: 81 outliers final: 49 residues processed: 351 average time/residue: 1.8271 time to fit residues: 751.4124 Evaluate side-chains 344 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 66 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 12 optimal weight: 0.0060 chunk 96 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121586 restraints weight = 26335.022| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.78 r_work: 0.3168 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26486 Z= 0.126 Angle : 0.547 13.578 36360 Z= 0.287 Chirality : 0.042 0.185 4172 Planarity : 0.004 0.049 4401 Dihedral : 16.639 177.510 4667 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 3.10 % Allowed : 17.89 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3032 helix: 1.49 (0.16), residues: 1094 sheet: -0.01 (0.26), residues: 428 loop : -0.89 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.002 0.001 HIS D 689 PHE 0.028 0.001 PHE D 70 TYR 0.014 0.001 TYR E 67 ARG 0.008 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1087) hydrogen bonds : angle 4.12832 ( 3007) metal coordination : bond 0.00321 ( 8) metal coordination : angle 2.13570 ( 12) covalent geometry : bond 0.00291 (26478) covalent geometry : angle 0.54601 (36348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 2.726 Fit side-chains revert: symmetry clash REVERT: Z 113 MET cc_start: 0.9134 (ptt) cc_final: 0.8834 (ptt) REVERT: A 137 GLU cc_start: 0.8131 (pp20) cc_final: 0.7782 (pp20) REVERT: B 2 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7989 (mm) REVERT: B 177 LYS cc_start: 0.8006 (mttp) cc_final: 0.7568 (tttp) REVERT: B 224 GLU cc_start: 0.7266 (pp20) cc_final: 0.6968 (pp20) REVERT: C 121 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7263 (mp0) REVERT: C 252 PHE cc_start: 0.8299 (m-80) cc_final: 0.8095 (m-80) REVERT: C 303 GLU cc_start: 0.7252 (pm20) cc_final: 0.6166 (tp30) REVERT: C 429 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6750 (tp30) REVERT: C 450 THR cc_start: 0.9027 (m) cc_final: 0.8822 (m) REVERT: C 467 ARG cc_start: 0.7014 (mpt-90) cc_final: 0.6558 (mpt-90) REVERT: C 584 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6801 (ptp-110) REVERT: C 645 GLU cc_start: 0.8378 (tt0) cc_final: 0.8054 (mt-10) REVERT: C 672 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: C 697 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: C 758 ASP cc_start: 0.8496 (p0) cc_final: 0.8144 (p0) REVERT: C 843 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 885 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8793 (mt) REVERT: C 947 ASP cc_start: 0.7512 (p0) cc_final: 0.7153 (p0) REVERT: C 982 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: C 1051 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: D 35 ASN cc_start: 0.7674 (t0) cc_final: 0.7246 (t0) REVERT: D 39 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7509 (mp) REVERT: D 123 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7804 (mmtm) REVERT: D 177 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.3489 (mm) REVERT: D 215 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: D 236 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6372 (m) REVERT: D 238 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7020 (tm-30) REVERT: D 248 TYR cc_start: 0.7450 (m-80) cc_final: 0.7227 (m-80) REVERT: D 250 GLU cc_start: 0.7073 (tp30) cc_final: 0.6653 (mm-30) REVERT: D 285 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5764 (ptpp) REVERT: D 356 ARG cc_start: 0.7678 (ttt90) cc_final: 0.6747 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7689 (p) REVERT: D 1087 ARG cc_start: 0.7006 (mmm-85) cc_final: 0.6701 (mtp85) REVERT: D 1112 MET cc_start: 0.7729 (mmm) cc_final: 0.7418 (mtp) REVERT: D 1113 GLU cc_start: 0.7762 (tt0) cc_final: 0.7330 (tp30) REVERT: D 1117 ASP cc_start: 0.7759 (p0) cc_final: 0.7425 (p0) REVERT: D 1137 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: D 1265 ASN cc_start: 0.8200 (m-40) cc_final: 0.7775 (m-40) REVERT: E 66 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7318 (m-30) outliers start: 79 outliers final: 51 residues processed: 334 average time/residue: 1.4326 time to fit residues: 557.3293 Evaluate side-chains 336 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 66 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 103 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121963 restraints weight = 26060.055| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.79 r_work: 0.3175 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26486 Z= 0.120 Angle : 0.542 13.375 36360 Z= 0.285 Chirality : 0.042 0.188 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.620 177.388 4665 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 2.82 % Allowed : 18.48 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3032 helix: 1.52 (0.16), residues: 1095 sheet: 0.02 (0.26), residues: 428 loop : -0.88 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.002 0.001 HIS D 94 PHE 0.029 0.001 PHE D 70 TYR 0.016 0.001 TYR E 67 ARG 0.007 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1087) hydrogen bonds : angle 4.10648 ( 3007) metal coordination : bond 0.00317 ( 8) metal coordination : angle 2.13629 ( 12) covalent geometry : bond 0.00273 (26478) covalent geometry : angle 0.54027 (36348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 2.542 Fit side-chains revert: symmetry clash REVERT: Z 113 MET cc_start: 0.9125 (ptt) cc_final: 0.8830 (ptt) REVERT: A 84 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 137 GLU cc_start: 0.8130 (pp20) cc_final: 0.7779 (pp20) REVERT: B 177 LYS cc_start: 0.7994 (mttp) cc_final: 0.7560 (tttp) REVERT: B 224 GLU cc_start: 0.7282 (pp20) cc_final: 0.6929 (pp20) REVERT: C 121 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7244 (mp0) REVERT: C 303 GLU cc_start: 0.7250 (pm20) cc_final: 0.6212 (tp30) REVERT: C 354 THR cc_start: 0.8747 (p) cc_final: 0.8530 (t) REVERT: C 429 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6730 (tp30) REVERT: C 450 THR cc_start: 0.9021 (m) cc_final: 0.8802 (m) REVERT: C 467 ARG cc_start: 0.7018 (mpt-90) cc_final: 0.6579 (mpt-90) REVERT: C 584 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6794 (ptp-110) REVERT: C 645 GLU cc_start: 0.8377 (tt0) cc_final: 0.8054 (mt-10) REVERT: C 697 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: C 758 ASP cc_start: 0.8479 (p0) cc_final: 0.8140 (p0) REVERT: C 843 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 885 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8788 (mt) REVERT: C 947 ASP cc_start: 0.7497 (p0) cc_final: 0.7142 (p0) REVERT: C 982 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: C 1051 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: D 35 ASN cc_start: 0.7696 (t0) cc_final: 0.7263 (t0) REVERT: D 39 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7560 (mp) REVERT: D 123 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7706 (mmtm) REVERT: D 177 LEU cc_start: 0.4290 (OUTLIER) cc_final: 0.3534 (mm) REVERT: D 215 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: D 236 VAL cc_start: 0.6682 (OUTLIER) cc_final: 0.6345 (m) REVERT: D 238 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6857 (tm-30) REVERT: D 248 TYR cc_start: 0.7411 (m-80) cc_final: 0.7190 (m-80) REVERT: D 356 ARG cc_start: 0.7677 (ttt90) cc_final: 0.6749 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7685 (p) REVERT: D 1087 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6726 (mtp85) REVERT: D 1112 MET cc_start: 0.7805 (mmm) cc_final: 0.7476 (mtp) REVERT: D 1113 GLU cc_start: 0.7748 (tt0) cc_final: 0.7324 (tp30) REVERT: D 1117 ASP cc_start: 0.7758 (p0) cc_final: 0.7423 (p0) REVERT: D 1137 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: D 1265 ASN cc_start: 0.8162 (m-40) cc_final: 0.7746 (m-40) REVERT: E 66 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7306 (m-30) outliers start: 72 outliers final: 51 residues processed: 324 average time/residue: 1.3973 time to fit residues: 524.7561 Evaluate side-chains 335 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 66 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120203 restraints weight = 26425.909| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.75 r_work: 0.3144 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26486 Z= 0.151 Angle : 0.572 13.731 36360 Z= 0.300 Chirality : 0.043 0.183 4172 Planarity : 0.004 0.050 4401 Dihedral : 16.674 177.242 4665 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 2.71 % Allowed : 18.71 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3032 helix: 1.43 (0.16), residues: 1093 sheet: -0.04 (0.25), residues: 440 loop : -0.93 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.003 0.001 HIS C 476 PHE 0.028 0.001 PHE D 70 TYR 0.017 0.001 TYR A 168 ARG 0.007 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 1087) hydrogen bonds : angle 4.20205 ( 3007) metal coordination : bond 0.00336 ( 8) metal coordination : angle 2.18563 ( 12) covalent geometry : bond 0.00359 (26478) covalent geometry : angle 0.57081 (36348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20152.32 seconds wall clock time: 345 minutes 43.91 seconds (20743.91 seconds total)