Starting phenix.real_space_refine on Mon Sep 14 10:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039.map" model { file = "/net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ee8_9039/09_2026/6ee8_9039_neut.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18270 2.51 5 N 5323 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29784 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1228 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 109.432 60.877 82.960 1.00169.12 S ATOM 19692 SG CYS D 968 106.034 61.770 84.984 1.00174.51 S ATOM 19734 SG CYS D 975 106.982 63.228 81.798 1.00161.34 S ATOM 19752 SG CYS D 978 106.509 59.787 80.902 1.00164.55 S ATOM 12567 SG CYS D 60 80.575 107.049 123.762 1.00178.81 S ATOM 12585 SG CYS D 62 79.844 107.368 127.301 1.00173.66 S ATOM 12720 SG CYS D 78 82.010 104.201 126.479 1.00175.82 S Time building chain proxies: 5.37, per 1000 atoms: 0.18 Number of scatterers: 29784 At special positions: 0 Unit cell: (135.2, 180.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 125 15.00 Mg 1 11.99 O 5964 8.00 N 5323 7.00 C 18270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 44 sheets defined 42.7% alpha, 15.1% beta 56 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.785A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.910A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.540A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.443A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.570A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.720A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.954A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.511A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.644A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.558A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 removed outlier: 3.540A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.627A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.285A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.600A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.388A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 5.485A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.700A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.727A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.299A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.080A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.321A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 removed outlier: 3.584A pdb=" N GLY D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.553A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.044A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 removed outlier: 4.100A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.592A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.859A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.517A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.579A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.921A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.102A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.757A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.667A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.529A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.661A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 4.184A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.595A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.249A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.185A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.626A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.820A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.885A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.742A pdb=" N GLU M 156 " --> pdb=" O THR M 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.075A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.934A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 3.573A pdb=" N SER B 19 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.652A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.206A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.966A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.130A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.756A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 668 removed outlier: 6.840A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.896A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.623A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.582A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.532A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.605A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.942A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.195A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 236 removed outlier: 4.054A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.219A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.636A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.163A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 3.964A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1182 removed outlier: 6.540A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.913A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8051 1.33 - 1.45: 5583 1.45 - 1.57: 16486 1.57 - 1.69: 247 1.69 - 1.81: 175 Bond restraints: 30542 Sorted by residual: bond pdb=" C ARG C 421 " pdb=" N PRO C 422 " ideal model delta sigma weight residual 1.336 1.396 -0.061 1.23e-02 6.61e+03 2.42e+01 bond pdb=" C3' DT P 105 " pdb=" O3' DT P 105 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C3' DT O 42 " pdb=" O3' DT O 42 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C3' DG O 56 " pdb=" O3' DG O 56 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" CA ILE C 773 " pdb=" C ILE C 773 " ideal model delta sigma weight residual 1.524 1.480 0.045 1.05e-02 9.07e+03 1.80e+01 ... (remaining 30537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 41419 3.63 - 7.25: 442 7.25 - 10.88: 36 10.88 - 14.50: 6 14.50 - 18.13: 3 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.99 103.99 16.00 1.08e+00 8.57e-01 2.20e+02 angle pdb=" N LEU A 225 " pdb=" CA LEU A 225 " pdb=" C LEU A 225 " ideal model delta sigma weight residual 113.37 99.17 14.20 1.38e+00 5.25e-01 1.06e+02 angle pdb=" C ILE C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.84 129.19 -9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 142.39 -15.39 2.40e+00 1.74e-01 4.11e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 106.71 13.89 2.20e+00 2.07e-01 3.98e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 17556 35.43 - 70.86: 755 70.86 - 106.29: 11 106.29 - 141.72: 0 141.72 - 177.15: 5 Dihedral angle restraints: 18327 sinusoidal: 8279 harmonic: 10048 Sorted by residual: dihedral pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual 122.80 138.78 -15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C GLU A 224 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual -122.60 -137.99 15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" CA VAL D 4 " pdb=" C VAL D 4 " pdb=" N ASN D 5 " pdb=" CA ASN D 5 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 18324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4695 0.150 - 0.300: 74 0.300 - 0.450: 3 0.450 - 0.600: 1 0.600 - 0.750: 2 Chirality restraints: 4775 Sorted by residual: chirality pdb=" CA GLU A 224 " pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CB GLU A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU A 221 " pdb=" CB LEU A 221 " pdb=" CD1 LEU A 221 " pdb=" CD2 LEU A 221 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ARG A 223 " pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CB ARG A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 4772 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG M 75 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C ARG M 75 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG M 75 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA M 76 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 56 " -0.031 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR E 56 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR E 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR E 56 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 56 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 21 " 0.039 2.00e-02 2.50e+03 1.65e-02 8.19e+00 pdb=" N9 DG O 21 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 21 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DG O 21 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG O 21 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG O 21 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG O 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG O 21 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG O 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG O 21 " -0.004 2.00e-02 2.50e+03 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 571 2.65 - 3.21: 26564 3.21 - 3.77: 50049 3.77 - 4.34: 63859 4.34 - 4.90: 99898 Nonbonded interactions: 240941 Sorted by model distance: nonbonded pdb=" NH2 ARG F 502 " pdb=" OP2 DT O 23 " model vdw 2.082 3.120 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.099 2.170 nonbonded pdb=" O GLY D 408 " pdb=" NH1 ARG D 414 " model vdw 2.120 3.120 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.126 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.129 2.170 ... (remaining 240936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 30.610 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.224 30549 Z= 0.428 Angle : 1.086 32.885 41912 Z= 0.672 Chirality : 0.059 0.750 4775 Planarity : 0.007 0.060 5070 Dihedral : 16.003 177.146 11863 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer: Outliers : 0.65 % Allowed : 5.01 % Favored : 94.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.12), residues: 3488 helix: -1.64 (0.11), residues: 1366 sheet: -2.12 (0.25), residues: 349 loop : -2.50 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 556 TYR 0.053 0.003 TYR E 56 PHE 0.042 0.003 PHE D 6 TRP 0.035 0.004 TRP C 70 HIS 0.014 0.003 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.42 (30542) covalent geometry : angle 1.06592 / 0.67 (41906) hydrogen bonds : bond 0.16934 / 11.51 ( 1363) hydrogen bonds : angle 7.14610 / 4.99 ( 3794) metal coordination : bond 0.14718 / 7.42 ( 7) metal coordination : angle 17.26583 / 8.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8782 (ptp) cc_final: 0.8582 (pmm) REVERT: B 191 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8709 (tttp) REVERT: B 226 ASN cc_start: 0.8834 (t160) cc_final: 0.8563 (t0) REVERT: C 202 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (m) REVERT: C 355 MET cc_start: 0.8995 (tmm) cc_final: 0.8686 (tmm) REVERT: C 396 MET cc_start: 0.9463 (tmt) cc_final: 0.8889 (tmm) REVERT: C 607 MET cc_start: 0.8781 (mtt) cc_final: 0.8495 (mtm) REVERT: C 611 MET cc_start: 0.9310 (mtm) cc_final: 0.8940 (ptp) REVERT: C 630 MET cc_start: 0.8955 (mmm) cc_final: 0.8667 (mmm) REVERT: C 733 ASP cc_start: 0.8636 (m-30) cc_final: 0.8399 (p0) REVERT: C 1038 ASP cc_start: 0.9185 (m-30) cc_final: 0.8738 (p0) REVERT: C 1088 LEU cc_start: 0.9545 (mt) cc_final: 0.9286 (pp) REVERT: C 1119 GLU cc_start: 0.8715 (tp30) cc_final: 0.8385 (tp30) REVERT: D 114 LEU cc_start: 0.9559 (mt) cc_final: 0.9176 (mt) REVERT: D 256 MET cc_start: 0.8351 (ttm) cc_final: 0.7784 (ttm) REVERT: D 373 MET cc_start: 0.8987 (mtp) cc_final: 0.8760 (mtp) REVERT: D 491 ILE cc_start: 0.9579 (mt) cc_final: 0.9362 (pt) REVERT: D 541 MET cc_start: 0.8606 (mtp) cc_final: 0.8069 (mtp) REVERT: D 1112 MET cc_start: 0.7305 (mmm) cc_final: 0.6858 (mmm) REVERT: E 41 ASP cc_start: 0.8792 (m-30) cc_final: 0.8444 (m-30) REVERT: E 42 GLU cc_start: 0.9539 (mt-10) cc_final: 0.8750 (tp30) REVERT: E 66 ASP cc_start: 0.9148 (m-30) cc_final: 0.8946 (t0) REVERT: E 105 GLU cc_start: 0.8676 (pt0) cc_final: 0.8440 (pt0) outliers start: 19 outliers final: 7 residues processed: 237 average time/residue: 0.1960 time to fit residues: 73.0287 Evaluate side-chains 131 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 578 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS B 124 HIS B 151 GLN B 185 GLN B 226 ASN C 81 ASN C 141 ASN C 142 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN C 729 HIS C 875 GLN C 920 HIS C1066 GLN D 22 GLN D 239 ASN D 307 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 564 ASN D 687 GLN D 693 GLN D 771 ASN D 797 ASN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN D1145 GLN D1190 ASN E 65 ASN E 69 ASN F 516 HIS J 36 ASN M 13 HIS M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.026472 restraints weight = 256643.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027298 restraints weight = 140808.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.027861 restraints weight = 94439.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.028217 restraints weight = 71734.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.028488 restraints weight = 59775.152| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 30549 Z= 0.282 Angle : 0.783 12.225 41912 Z= 0.414 Chirality : 0.047 0.346 4775 Planarity : 0.006 0.098 5070 Dihedral : 19.863 172.420 5217 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 1.71 % Allowed : 8.23 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3488 helix: -0.08 (0.13), residues: 1400 sheet: -1.71 (0.27), residues: 321 loop : -1.95 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 223 TYR 0.039 0.002 TYR E 56 PHE 0.021 0.002 PHE D 6 TRP 0.019 0.002 TRP C 70 HIS 0.007 0.002 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (30542) covalent geometry : angle 0.78167 / 0.41 (41906) hydrogen bonds : bond 0.05395 / 3.68 ( 1363) hydrogen bonds : angle 5.58375 / 3.88 ( 3794) metal coordination : bond 0.01703 / 0.91 ( 7) metal coordination : angle 4.40256 / 2.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8757 (ttm) cc_final: 0.8431 (tmm) REVERT: B 1 MET cc_start: 0.8451 (tpp) cc_final: 0.7906 (tpp) REVERT: B 191 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8696 (tttp) REVERT: B 226 ASN cc_start: 0.8763 (t0) cc_final: 0.8517 (t0) REVERT: C 103 MET cc_start: 0.9441 (ptp) cc_final: 0.8803 (ppp) REVERT: C 122 CYS cc_start: 0.9382 (m) cc_final: 0.9114 (m) REVERT: C 355 MET cc_start: 0.8928 (tmm) cc_final: 0.8667 (tmm) REVERT: C 393 MET cc_start: 0.9229 (tpp) cc_final: 0.8881 (mmm) REVERT: C 586 MET cc_start: 0.8781 (ppp) cc_final: 0.7670 (ppp) REVERT: C 607 MET cc_start: 0.8876 (mtt) cc_final: 0.8541 (mtm) REVERT: C 611 MET cc_start: 0.9184 (mtm) cc_final: 0.8787 (ptp) REVERT: C 630 MET cc_start: 0.8820 (mmm) cc_final: 0.8606 (mmp) REVERT: C 661 MET cc_start: 0.8906 (tpt) cc_final: 0.8537 (tpt) REVERT: C 1038 ASP cc_start: 0.9171 (m-30) cc_final: 0.8753 (p0) REVERT: C 1119 GLU cc_start: 0.8699 (tp30) cc_final: 0.8292 (tp30) REVERT: D 114 LEU cc_start: 0.9532 (mt) cc_final: 0.9145 (mt) REVERT: D 143 MET cc_start: 0.9493 (mtp) cc_final: 0.9222 (mtp) REVERT: D 256 MET cc_start: 0.8345 (ttm) cc_final: 0.7656 (ttm) REVERT: D 327 MET cc_start: 0.8597 (tpp) cc_final: 0.8389 (tpt) REVERT: D 491 ILE cc_start: 0.9616 (mt) cc_final: 0.9393 (pt) REVERT: D 733 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8451 (tmm) REVERT: D 1112 MET cc_start: 0.7903 (mmm) cc_final: 0.7558 (mmm) REVERT: E 41 ASP cc_start: 0.8669 (m-30) cc_final: 0.8412 (m-30) REVERT: E 42 GLU cc_start: 0.9615 (mt-10) cc_final: 0.8989 (tp30) REVERT: E 78 TYR cc_start: 0.8166 (m-10) cc_final: 0.7861 (m-10) REVERT: F 282 MET cc_start: 0.9382 (mmm) cc_final: 0.9135 (mmm) REVERT: J 86 LEU cc_start: 0.9804 (OUTLIER) cc_final: 0.9522 (pp) outliers start: 50 outliers final: 15 residues processed: 172 average time/residue: 0.1832 time to fit residues: 51.6255 Evaluate side-chains 133 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 351 optimal weight: 0.7980 chunk 345 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN C1066 GLN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.026628 restraints weight = 254965.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027470 restraints weight = 138915.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.028031 restraints weight = 92556.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028402 restraints weight = 70365.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.028667 restraints weight = 58571.184| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30549 Z= 0.190 Angle : 0.677 11.259 41912 Z= 0.357 Chirality : 0.045 0.379 4775 Planarity : 0.005 0.058 5070 Dihedral : 19.655 178.759 5209 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 1.58 % Allowed : 8.78 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3488 helix: 0.52 (0.14), residues: 1406 sheet: -1.51 (0.27), residues: 319 loop : -1.75 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 636 TYR 0.036 0.002 TYR E 56 PHE 0.021 0.001 PHE D 6 TRP 0.018 0.002 TRP D 223 HIS 0.005 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (30542) covalent geometry : angle 0.67506 / 0.36 (41906) hydrogen bonds : bond 0.04710 / 3.21 ( 1363) hydrogen bonds : angle 5.13203 / 3.58 ( 3794) metal coordination : bond 0.00597 / 0.29 ( 7) metal coordination : angle 3.77055 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8869 (ttm) cc_final: 0.8388 (tmm) REVERT: B 1 MET cc_start: 0.8468 (tpp) cc_final: 0.7917 (tpp) REVERT: B 191 LYS cc_start: 0.9244 (ttpt) cc_final: 0.8678 (tttp) REVERT: B 226 ASN cc_start: 0.8746 (t0) cc_final: 0.8534 (t0) REVERT: C 103 MET cc_start: 0.9407 (ptp) cc_final: 0.8800 (ppp) REVERT: C 122 CYS cc_start: 0.9284 (m) cc_final: 0.9040 (m) REVERT: C 355 MET cc_start: 0.8953 (tmm) cc_final: 0.8611 (tmm) REVERT: C 393 MET cc_start: 0.9301 (tpp) cc_final: 0.8986 (mmm) REVERT: C 404 MET cc_start: 0.8565 (ptt) cc_final: 0.8211 (ptp) REVERT: C 561 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8696 (p) REVERT: C 586 MET cc_start: 0.8967 (ppp) cc_final: 0.7666 (ppp) REVERT: C 607 MET cc_start: 0.8900 (mtt) cc_final: 0.8573 (mtm) REVERT: C 611 MET cc_start: 0.9125 (mtm) cc_final: 0.8742 (ptp) REVERT: C 630 MET cc_start: 0.8888 (mmm) cc_final: 0.8622 (mmm) REVERT: C 661 MET cc_start: 0.8794 (tpt) cc_final: 0.8439 (tpt) REVERT: C 1038 ASP cc_start: 0.9126 (m-30) cc_final: 0.8742 (p0) REVERT: C 1119 GLU cc_start: 0.8693 (tp30) cc_final: 0.8251 (tp30) REVERT: D 114 LEU cc_start: 0.9553 (mt) cc_final: 0.9184 (mt) REVERT: D 143 MET cc_start: 0.9491 (mtp) cc_final: 0.9203 (mtp) REVERT: D 155 MET cc_start: 0.8659 (tpt) cc_final: 0.8455 (tmm) REVERT: D 229 LEU cc_start: 0.9454 (mt) cc_final: 0.9106 (mt) REVERT: D 256 MET cc_start: 0.8251 (ttm) cc_final: 0.7729 (ttm) REVERT: D 373 MET cc_start: 0.8784 (mtp) cc_final: 0.8137 (ptp) REVERT: D 491 ILE cc_start: 0.9590 (mt) cc_final: 0.9344 (pt) REVERT: D 516 LEU cc_start: 0.9301 (mt) cc_final: 0.8978 (mt) REVERT: D 733 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8418 (tmm) REVERT: D 983 MET cc_start: 0.8356 (tpp) cc_final: 0.8119 (tpp) REVERT: D 1112 MET cc_start: 0.7866 (mmm) cc_final: 0.7469 (mmm) REVERT: E 41 ASP cc_start: 0.8667 (m-30) cc_final: 0.8401 (m-30) REVERT: E 42 GLU cc_start: 0.9557 (mt-10) cc_final: 0.8927 (tp30) REVERT: J 86 LEU cc_start: 0.9793 (OUTLIER) cc_final: 0.9539 (pp) REVERT: M 11 TYR cc_start: 0.9153 (t80) cc_final: 0.8289 (t80) REVERT: M 55 TYR cc_start: 0.8269 (m-80) cc_final: 0.7953 (m-80) outliers start: 46 outliers final: 23 residues processed: 161 average time/residue: 0.1678 time to fit residues: 45.3461 Evaluate side-chains 142 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 160 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 261 optimal weight: 0.0060 chunk 336 optimal weight: 30.0000 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 HIS ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.036204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.026795 restraints weight = 252142.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.027637 restraints weight = 138446.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.028198 restraints weight = 92453.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.028576 restraints weight = 70263.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.028804 restraints weight = 58380.977| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30549 Z= 0.163 Angle : 0.636 9.623 41912 Z= 0.336 Chirality : 0.044 0.382 4775 Planarity : 0.004 0.059 5070 Dihedral : 19.522 179.389 5207 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.06 % Allowed : 9.02 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3488 helix: 0.83 (0.14), residues: 1407 sheet: -1.31 (0.28), residues: 321 loop : -1.65 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1143 TYR 0.030 0.001 TYR E 56 PHE 0.018 0.001 PHE D 6 TRP 0.013 0.001 TRP C 70 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (30542) covalent geometry : angle 0.63521 / 0.34 (41906) hydrogen bonds : bond 0.04278 / 2.92 ( 1363) hydrogen bonds : angle 4.87367 / 3.41 ( 3794) metal coordination : bond 0.00533 / 0.26 ( 7) metal coordination : angle 3.22188 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8956 (ttm) cc_final: 0.8563 (tmm) REVERT: B 1 MET cc_start: 0.8516 (tpp) cc_final: 0.7954 (tpp) REVERT: B 173 LYS cc_start: 0.9079 (tptp) cc_final: 0.8742 (tptp) REVERT: B 191 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8644 (tttp) REVERT: B 226 ASN cc_start: 0.8735 (t0) cc_final: 0.8515 (t0) REVERT: C 103 MET cc_start: 0.9366 (ptp) cc_final: 0.8813 (ppp) REVERT: C 122 CYS cc_start: 0.9239 (m) cc_final: 0.8962 (m) REVERT: C 355 MET cc_start: 0.8809 (tmm) cc_final: 0.8579 (tmm) REVERT: C 393 MET cc_start: 0.9404 (tpp) cc_final: 0.9164 (mmm) REVERT: C 404 MET cc_start: 0.8613 (ptt) cc_final: 0.8215 (ptp) REVERT: C 561 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 586 MET cc_start: 0.9118 (ppp) cc_final: 0.7632 (ppp) REVERT: C 607 MET cc_start: 0.9020 (mtt) cc_final: 0.8574 (mtm) REVERT: C 611 MET cc_start: 0.9232 (mtm) cc_final: 0.8694 (ptp) REVERT: C 630 MET cc_start: 0.8898 (mmm) cc_final: 0.8630 (mmm) REVERT: C 661 MET cc_start: 0.8839 (tpt) cc_final: 0.8472 (tpt) REVERT: C 784 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9049 (pp) REVERT: C 907 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9056 (tm) REVERT: C 1038 ASP cc_start: 0.9154 (m-30) cc_final: 0.8795 (p0) REVERT: C 1051 MET cc_start: 0.9027 (tpt) cc_final: 0.8646 (tpp) REVERT: C 1119 GLU cc_start: 0.8715 (tp30) cc_final: 0.8278 (tp30) REVERT: D 114 LEU cc_start: 0.9523 (mt) cc_final: 0.9129 (mt) REVERT: D 143 MET cc_start: 0.9515 (mtp) cc_final: 0.9277 (mtp) REVERT: D 155 MET cc_start: 0.8658 (tpt) cc_final: 0.8447 (tmm) REVERT: D 229 LEU cc_start: 0.9460 (mt) cc_final: 0.9113 (mt) REVERT: D 256 MET cc_start: 0.8040 (ttm) cc_final: 0.7485 (ttm) REVERT: D 373 MET cc_start: 0.8739 (mtp) cc_final: 0.8393 (ptp) REVERT: D 491 ILE cc_start: 0.9595 (mt) cc_final: 0.9303 (pt) REVERT: D 516 LEU cc_start: 0.9447 (mt) cc_final: 0.9136 (mt) REVERT: D 706 MET cc_start: 0.9222 (mmm) cc_final: 0.8891 (mmm) REVERT: D 733 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8413 (tmm) REVERT: D 983 MET cc_start: 0.8309 (tpp) cc_final: 0.8037 (tpp) REVERT: D 991 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 1012 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8755 (ppp) REVERT: D 1112 MET cc_start: 0.7793 (mmm) cc_final: 0.7287 (mmm) REVERT: E 41 ASP cc_start: 0.8759 (m-30) cc_final: 0.8505 (m-30) REVERT: E 42 GLU cc_start: 0.9579 (mt-10) cc_final: 0.8938 (tp30) REVERT: J 60 MET cc_start: 0.8176 (ppp) cc_final: 0.7043 (ppp) REVERT: J 69 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8357 (tm) REVERT: J 86 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9572 (pp) REVERT: M 11 TYR cc_start: 0.9152 (t80) cc_final: 0.8315 (t80) REVERT: M 55 TYR cc_start: 0.8191 (m-80) cc_final: 0.7917 (m-80) outliers start: 60 outliers final: 35 residues processed: 171 average time/residue: 0.1728 time to fit residues: 49.9573 Evaluate side-chains 156 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 78 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 60 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026239 restraints weight = 256286.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.027052 restraints weight = 141454.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.027606 restraints weight = 95190.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027966 restraints weight = 72516.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.028231 restraints weight = 60594.849| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30549 Z= 0.228 Angle : 0.672 10.268 41912 Z= 0.352 Chirality : 0.044 0.390 4775 Planarity : 0.004 0.061 5070 Dihedral : 19.463 179.302 5207 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.13 % Allowed : 9.08 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3488 helix: 0.98 (0.14), residues: 1410 sheet: -1.22 (0.28), residues: 320 loop : -1.57 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 301 TYR 0.030 0.002 TYR E 56 PHE 0.018 0.002 PHE D 6 TRP 0.013 0.002 TRP J 82 HIS 0.006 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (30542) covalent geometry : angle 0.67140 / 0.35 (41906) hydrogen bonds : bond 0.04670 / 3.19 ( 1363) hydrogen bonds : angle 4.86446 / 3.40 ( 3794) metal coordination : bond 0.00968 / 0.50 ( 7) metal coordination : angle 3.25596 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 115 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8977 (ttm) cc_final: 0.8593 (tmm) REVERT: B 1 MET cc_start: 0.8553 (tpp) cc_final: 0.7942 (tpp) REVERT: B 173 LYS cc_start: 0.9094 (tptp) cc_final: 0.8843 (tptp) REVERT: B 177 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8050 (ptmm) REVERT: B 191 LYS cc_start: 0.9244 (ttpt) cc_final: 0.8660 (tttp) REVERT: C 103 MET cc_start: 0.9344 (ptp) cc_final: 0.8768 (ppp) REVERT: C 122 CYS cc_start: 0.9133 (m) cc_final: 0.8913 (m) REVERT: C 159 MET cc_start: 0.9322 (tpp) cc_final: 0.8817 (mmm) REVERT: C 355 MET cc_start: 0.8786 (tmm) cc_final: 0.8535 (tmm) REVERT: C 393 MET cc_start: 0.9414 (tpp) cc_final: 0.9007 (tpp) REVERT: C 396 MET cc_start: 0.9433 (tmt) cc_final: 0.9102 (tmm) REVERT: C 404 MET cc_start: 0.8637 (ptt) cc_final: 0.8324 (ptp) REVERT: C 586 MET cc_start: 0.9211 (ppp) cc_final: 0.8110 (ppp) REVERT: C 607 MET cc_start: 0.9011 (mtt) cc_final: 0.8540 (mtm) REVERT: C 611 MET cc_start: 0.9235 (mtm) cc_final: 0.8754 (mtp) REVERT: C 661 MET cc_start: 0.8959 (tpt) cc_final: 0.8527 (tpt) REVERT: C 784 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9079 (pp) REVERT: C 907 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9107 (tm) REVERT: C 1038 ASP cc_start: 0.9126 (m-30) cc_final: 0.8860 (p0) REVERT: C 1076 MET cc_start: 0.9324 (mmm) cc_final: 0.8888 (mmm) REVERT: C 1119 GLU cc_start: 0.8747 (tp30) cc_final: 0.8331 (tp30) REVERT: D 143 MET cc_start: 0.9498 (mtp) cc_final: 0.9238 (mtp) REVERT: D 155 MET cc_start: 0.8658 (tpt) cc_final: 0.8437 (tmm) REVERT: D 229 LEU cc_start: 0.9497 (mt) cc_final: 0.9097 (mt) REVERT: D 256 MET cc_start: 0.8076 (ttm) cc_final: 0.7504 (ttm) REVERT: D 312 MET cc_start: 0.9125 (mmm) cc_final: 0.8923 (tpp) REVERT: D 373 MET cc_start: 0.8704 (mtp) cc_final: 0.8339 (ptp) REVERT: D 491 ILE cc_start: 0.9620 (mt) cc_final: 0.9415 (pt) REVERT: D 733 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8452 (tmm) REVERT: D 983 MET cc_start: 0.8285 (tpp) cc_final: 0.8077 (tpt) REVERT: D 991 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8692 (tp) REVERT: D 1112 MET cc_start: 0.7799 (mmm) cc_final: 0.7521 (mmm) REVERT: E 41 ASP cc_start: 0.8776 (m-30) cc_final: 0.8552 (m-30) REVERT: E 42 GLU cc_start: 0.9571 (mt-10) cc_final: 0.8940 (tp30) REVERT: J 69 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8286 (tm) REVERT: J 86 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9572 (pp) REVERT: M 11 TYR cc_start: 0.9152 (t80) cc_final: 0.8330 (t80) REVERT: M 55 TYR cc_start: 0.8325 (m-80) cc_final: 0.8101 (m-80) outliers start: 62 outliers final: 41 residues processed: 172 average time/residue: 0.1643 time to fit residues: 47.6965 Evaluate side-chains 156 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 331 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.035536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.026185 restraints weight = 256349.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.027001 restraints weight = 141656.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.027553 restraints weight = 95198.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027923 restraints weight = 72620.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.028156 restraints weight = 60691.650| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 30549 Z= 0.232 Angle : 0.675 11.505 41912 Z= 0.353 Chirality : 0.045 0.386 4775 Planarity : 0.004 0.061 5070 Dihedral : 19.399 179.597 5207 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.40 % Allowed : 9.67 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3488 helix: 1.06 (0.14), residues: 1415 sheet: -1.07 (0.28), residues: 329 loop : -1.58 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 480 TYR 0.028 0.002 TYR E 56 PHE 0.017 0.002 PHE C 61 TRP 0.013 0.002 TRP J 82 HIS 0.006 0.001 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (30542) covalent geometry : angle 0.67386 / 0.35 (41906) hydrogen bonds : bond 0.04556 / 3.11 ( 1363) hydrogen bonds : angle 4.82591 / 3.37 ( 3794) metal coordination : bond 0.00927 / 0.48 ( 7) metal coordination : angle 3.29238 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 110 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8588 (tpp) cc_final: 0.7947 (tpp) REVERT: B 173 LYS cc_start: 0.9100 (tptp) cc_final: 0.8659 (tptp) REVERT: B 177 LYS cc_start: 0.8774 (ptmm) cc_final: 0.8050 (ptmm) REVERT: B 191 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8652 (tttp) REVERT: C 122 CYS cc_start: 0.9109 (m) cc_final: 0.8888 (m) REVERT: C 159 MET cc_start: 0.9332 (tpp) cc_final: 0.8801 (mmm) REVERT: C 355 MET cc_start: 0.8774 (tmm) cc_final: 0.8506 (tmm) REVERT: C 393 MET cc_start: 0.9418 (tpp) cc_final: 0.9017 (tpp) REVERT: C 396 MET cc_start: 0.9433 (tmt) cc_final: 0.9122 (tmm) REVERT: C 586 MET cc_start: 0.9261 (ppp) cc_final: 0.8249 (ppp) REVERT: C 607 MET cc_start: 0.9007 (mtt) cc_final: 0.8537 (mtm) REVERT: C 611 MET cc_start: 0.9221 (mtm) cc_final: 0.8742 (mtp) REVERT: C 661 MET cc_start: 0.8955 (tpt) cc_final: 0.8524 (tpt) REVERT: C 784 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9063 (pp) REVERT: C 907 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9116 (tm) REVERT: C 1051 MET cc_start: 0.9109 (tpt) cc_final: 0.8841 (mmm) REVERT: C 1076 MET cc_start: 0.9358 (mmm) cc_final: 0.8936 (mmm) REVERT: C 1119 GLU cc_start: 0.8733 (tp30) cc_final: 0.8379 (tp30) REVERT: D 143 MET cc_start: 0.9496 (mtp) cc_final: 0.9234 (mtp) REVERT: D 155 MET cc_start: 0.8648 (tpt) cc_final: 0.8431 (tmm) REVERT: D 229 LEU cc_start: 0.9518 (mt) cc_final: 0.9117 (mt) REVERT: D 256 MET cc_start: 0.8173 (ttm) cc_final: 0.7371 (mtp) REVERT: D 373 MET cc_start: 0.8741 (mtp) cc_final: 0.8367 (ptp) REVERT: D 491 ILE cc_start: 0.9656 (mt) cc_final: 0.9425 (pt) REVERT: D 516 LEU cc_start: 0.9503 (mt) cc_final: 0.9112 (pt) REVERT: D 706 MET cc_start: 0.9234 (mmm) cc_final: 0.8928 (mmm) REVERT: D 733 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8497 (tmm) REVERT: D 991 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8700 (tp) REVERT: D 1112 MET cc_start: 0.7813 (mmm) cc_final: 0.7252 (mmm) REVERT: E 41 ASP cc_start: 0.8771 (m-30) cc_final: 0.8529 (m-30) REVERT: E 42 GLU cc_start: 0.9573 (mt-10) cc_final: 0.8953 (tp30) REVERT: F 282 MET cc_start: 0.9287 (mmm) cc_final: 0.8992 (mmm) REVERT: J 60 MET cc_start: 0.8292 (ppp) cc_final: 0.6939 (ppp) REVERT: J 69 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8325 (tm) REVERT: J 86 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9559 (pp) REVERT: M 11 TYR cc_start: 0.9119 (t80) cc_final: 0.8361 (t80) REVERT: M 55 TYR cc_start: 0.8374 (m-80) cc_final: 0.8108 (m-80) outliers start: 70 outliers final: 49 residues processed: 171 average time/residue: 0.1726 time to fit residues: 49.2794 Evaluate side-chains 163 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 0.0980 chunk 281 optimal weight: 7.9990 chunk 270 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.026146 restraints weight = 256736.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.026964 restraints weight = 141865.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027522 restraints weight = 95461.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027875 restraints weight = 72749.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.028141 restraints weight = 60807.314| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30549 Z= 0.227 Angle : 0.674 12.318 41912 Z= 0.352 Chirality : 0.044 0.386 4775 Planarity : 0.004 0.061 5070 Dihedral : 19.348 179.546 5207 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.26 % Allowed : 10.08 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3488 helix: 1.17 (0.14), residues: 1416 sheet: -1.03 (0.28), residues: 330 loop : -1.51 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 278 TYR 0.028 0.002 TYR E 56 PHE 0.019 0.002 PHE C 61 TRP 0.014 0.002 TRP J 82 HIS 0.009 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (30542) covalent geometry : angle 0.67250 / 0.35 (41906) hydrogen bonds : bond 0.04542 / 3.10 ( 1363) hydrogen bonds : angle 4.78019 / 3.34 ( 3794) metal coordination : bond 0.00867 / 0.45 ( 7) metal coordination : angle 3.21321 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 112 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8609 (tpp) cc_final: 0.7894 (tpp) REVERT: B 173 LYS cc_start: 0.9066 (tptp) cc_final: 0.8620 (tptp) REVERT: B 177 LYS cc_start: 0.8785 (ptmm) cc_final: 0.8053 (ptmm) REVERT: B 191 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8656 (tttp) REVERT: C 103 MET cc_start: 0.9240 (ptm) cc_final: 0.8725 (ppp) REVERT: C 122 CYS cc_start: 0.9109 (m) cc_final: 0.8907 (m) REVERT: C 159 MET cc_start: 0.9318 (tpp) cc_final: 0.8808 (mmm) REVERT: C 355 MET cc_start: 0.8776 (tmm) cc_final: 0.8501 (tmm) REVERT: C 393 MET cc_start: 0.9413 (tpp) cc_final: 0.9028 (tpp) REVERT: C 396 MET cc_start: 0.9423 (tmt) cc_final: 0.9106 (tmm) REVERT: C 404 MET cc_start: 0.8612 (ptp) cc_final: 0.8331 (ptp) REVERT: C 412 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8934 (mm) REVERT: C 586 MET cc_start: 0.9277 (ppp) cc_final: 0.8275 (ppp) REVERT: C 607 MET cc_start: 0.9003 (mtt) cc_final: 0.8530 (mtm) REVERT: C 611 MET cc_start: 0.9214 (mtm) cc_final: 0.8769 (mtp) REVERT: C 661 MET cc_start: 0.8941 (tpt) cc_final: 0.8503 (tpt) REVERT: C 784 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 907 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9122 (tm) REVERT: C 1051 MET cc_start: 0.9125 (tpt) cc_final: 0.8855 (mmm) REVERT: C 1076 MET cc_start: 0.9368 (mmm) cc_final: 0.8925 (mmm) REVERT: C 1119 GLU cc_start: 0.8743 (tp30) cc_final: 0.8397 (tp30) REVERT: D 143 MET cc_start: 0.9491 (mtp) cc_final: 0.9202 (mtp) REVERT: D 155 MET cc_start: 0.8656 (tpt) cc_final: 0.8448 (tmm) REVERT: D 229 LEU cc_start: 0.9532 (mt) cc_final: 0.9116 (mt) REVERT: D 256 MET cc_start: 0.8138 (ttm) cc_final: 0.7356 (mtp) REVERT: D 373 MET cc_start: 0.8787 (mtp) cc_final: 0.8484 (ptp) REVERT: D 491 ILE cc_start: 0.9661 (mt) cc_final: 0.9437 (pt) REVERT: D 516 LEU cc_start: 0.9527 (mt) cc_final: 0.9110 (pt) REVERT: D 706 MET cc_start: 0.9230 (mmm) cc_final: 0.8923 (mmm) REVERT: D 733 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8496 (tmm) REVERT: D 1112 MET cc_start: 0.7799 (mmm) cc_final: 0.7229 (mmm) REVERT: E 41 ASP cc_start: 0.8780 (m-30) cc_final: 0.8532 (m-30) REVERT: E 42 GLU cc_start: 0.9562 (mt-10) cc_final: 0.8930 (tp30) REVERT: F 282 MET cc_start: 0.9331 (mmm) cc_final: 0.8994 (mmm) REVERT: J 60 MET cc_start: 0.8403 (ppp) cc_final: 0.7114 (ppp) REVERT: J 69 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8288 (tm) REVERT: M 11 TYR cc_start: 0.9089 (t80) cc_final: 0.8343 (t80) REVERT: M 55 TYR cc_start: 0.8310 (m-80) cc_final: 0.7974 (m-80) outliers start: 66 outliers final: 49 residues processed: 172 average time/residue: 0.1759 time to fit residues: 50.7836 Evaluate side-chains 163 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 217 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 333 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.026252 restraints weight = 256096.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.027078 restraints weight = 141498.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.027640 restraints weight = 95092.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.028001 restraints weight = 72539.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.028269 restraints weight = 60498.146| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30549 Z= 0.194 Angle : 0.664 14.969 41912 Z= 0.345 Chirality : 0.044 0.385 4775 Planarity : 0.004 0.062 5070 Dihedral : 19.311 179.638 5207 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.02 % Allowed : 10.49 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3488 helix: 1.25 (0.14), residues: 1416 sheet: -0.90 (0.29), residues: 326 loop : -1.48 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 251 TYR 0.025 0.001 TYR E 56 PHE 0.018 0.001 PHE C 61 TRP 0.013 0.001 TRP J 82 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (30542) covalent geometry : angle 0.66262 / 0.35 (41906) hydrogen bonds : bond 0.04302 / 2.93 ( 1363) hydrogen bonds : angle 4.70762 / 3.30 ( 3794) metal coordination : bond 0.00675 / 0.34 ( 7) metal coordination : angle 3.14505 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8612 (tpp) cc_final: 0.7881 (tpp) REVERT: B 173 LYS cc_start: 0.9104 (tptp) cc_final: 0.8660 (tptp) REVERT: B 177 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8066 (ptmm) REVERT: B 191 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8653 (tttp) REVERT: C 103 MET cc_start: 0.9261 (ptm) cc_final: 0.8769 (ppp) REVERT: C 122 CYS cc_start: 0.9102 (m) cc_final: 0.8884 (m) REVERT: C 159 MET cc_start: 0.9324 (tpp) cc_final: 0.8828 (mmm) REVERT: C 355 MET cc_start: 0.8769 (tmm) cc_final: 0.8498 (tmm) REVERT: C 393 MET cc_start: 0.9418 (tpp) cc_final: 0.9022 (tpp) REVERT: C 396 MET cc_start: 0.9445 (tmt) cc_final: 0.9131 (tmm) REVERT: C 404 MET cc_start: 0.8550 (ptp) cc_final: 0.8283 (ptp) REVERT: C 412 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8946 (mm) REVERT: C 586 MET cc_start: 0.9280 (ppp) cc_final: 0.8289 (ppp) REVERT: C 607 MET cc_start: 0.8991 (mtt) cc_final: 0.8518 (mtm) REVERT: C 611 MET cc_start: 0.9204 (mtm) cc_final: 0.8787 (mtp) REVERT: C 661 MET cc_start: 0.8934 (tpt) cc_final: 0.8500 (tpt) REVERT: C 784 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9034 (pp) REVERT: C 907 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9106 (tm) REVERT: C 1051 MET cc_start: 0.9118 (tpt) cc_final: 0.8866 (mmm) REVERT: C 1076 MET cc_start: 0.9356 (mmm) cc_final: 0.8911 (mmm) REVERT: D 143 MET cc_start: 0.9484 (mtp) cc_final: 0.9196 (mtp) REVERT: D 155 MET cc_start: 0.8646 (tpt) cc_final: 0.8441 (tmm) REVERT: D 229 LEU cc_start: 0.9523 (mt) cc_final: 0.9093 (mt) REVERT: D 256 MET cc_start: 0.8214 (ttm) cc_final: 0.7454 (mtp) REVERT: D 373 MET cc_start: 0.8804 (mtp) cc_final: 0.8421 (ptp) REVERT: D 457 MET cc_start: 0.9323 (mtp) cc_final: 0.8825 (mmt) REVERT: D 491 ILE cc_start: 0.9665 (mt) cc_final: 0.9430 (pt) REVERT: D 516 LEU cc_start: 0.9542 (mt) cc_final: 0.9114 (pt) REVERT: D 581 MET cc_start: 0.8921 (pmm) cc_final: 0.8679 (pmm) REVERT: D 706 MET cc_start: 0.9221 (mmm) cc_final: 0.8910 (mmm) REVERT: D 733 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: D 975 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8768 (p) REVERT: D 1112 MET cc_start: 0.7781 (mmm) cc_final: 0.7210 (mmm) REVERT: E 41 ASP cc_start: 0.8824 (m-30) cc_final: 0.8586 (m-30) REVERT: E 42 GLU cc_start: 0.9560 (mt-10) cc_final: 0.8876 (tp30) REVERT: F 282 MET cc_start: 0.9350 (mmm) cc_final: 0.8979 (mmm) REVERT: J 60 MET cc_start: 0.8404 (ppp) cc_final: 0.7128 (ppp) REVERT: J 69 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (tm) REVERT: J 86 LEU cc_start: 0.9799 (OUTLIER) cc_final: 0.9572 (pp) REVERT: M 11 TYR cc_start: 0.9074 (t80) cc_final: 0.8333 (t80) REVERT: M 55 TYR cc_start: 0.8325 (m-80) cc_final: 0.7999 (m-80) outliers start: 59 outliers final: 49 residues processed: 167 average time/residue: 0.1802 time to fit residues: 50.4324 Evaluate side-chains 165 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 109 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 138 optimal weight: 0.0470 chunk 303 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.026536 restraints weight = 253694.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.027383 restraints weight = 138409.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027957 restraints weight = 92586.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.028327 restraints weight = 70264.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.028592 restraints weight = 58556.430| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30549 Z= 0.147 Angle : 0.633 12.655 41912 Z= 0.329 Chirality : 0.044 0.383 4775 Planarity : 0.004 0.062 5070 Dihedral : 19.251 179.647 5207 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.92 % Allowed : 10.66 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3488 helix: 1.36 (0.14), residues: 1419 sheet: -0.82 (0.29), residues: 321 loop : -1.37 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 109 TYR 0.024 0.001 TYR E 67 PHE 0.016 0.001 PHE C 61 TRP 0.014 0.001 TRP D 223 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (30542) covalent geometry : angle 0.63233 / 0.33 (41906) hydrogen bonds : bond 0.03948 / 2.69 ( 1363) hydrogen bonds : angle 4.57466 / 3.21 ( 3794) metal coordination : bond 0.00393 / 0.19 ( 7) metal coordination : angle 2.98450 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8957 (ttm) cc_final: 0.8592 (tmm) REVERT: B 1 MET cc_start: 0.8575 (tpp) cc_final: 0.7893 (tpp) REVERT: B 70 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8959 (ptpt) REVERT: B 173 LYS cc_start: 0.9097 (tptp) cc_final: 0.8648 (tptp) REVERT: B 177 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8173 (ptmm) REVERT: B 191 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8653 (tttp) REVERT: C 103 MET cc_start: 0.9261 (ptm) cc_final: 0.8767 (ppp) REVERT: C 159 MET cc_start: 0.9293 (tpp) cc_final: 0.8815 (mmm) REVERT: C 355 MET cc_start: 0.8802 (tmm) cc_final: 0.8468 (tmm) REVERT: C 393 MET cc_start: 0.9411 (tpp) cc_final: 0.9008 (tpp) REVERT: C 396 MET cc_start: 0.9423 (tmt) cc_final: 0.9116 (tmm) REVERT: C 404 MET cc_start: 0.8572 (ptp) cc_final: 0.8207 (ptt) REVERT: C 412 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 586 MET cc_start: 0.9284 (ppp) cc_final: 0.8288 (ppp) REVERT: C 607 MET cc_start: 0.8982 (mtt) cc_final: 0.8508 (mtm) REVERT: C 611 MET cc_start: 0.9183 (mtm) cc_final: 0.8777 (mtp) REVERT: C 661 MET cc_start: 0.8815 (tpt) cc_final: 0.8405 (tpt) REVERT: C 672 MET cc_start: 0.8837 (tpp) cc_final: 0.8539 (tpp) REVERT: C 784 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 907 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9036 (tm) REVERT: C 1051 MET cc_start: 0.9162 (tpt) cc_final: 0.8929 (mmm) REVERT: C 1076 MET cc_start: 0.9332 (mmm) cc_final: 0.8913 (mmm) REVERT: C 1119 GLU cc_start: 0.8699 (tp30) cc_final: 0.8315 (tp30) REVERT: D 143 MET cc_start: 0.9483 (mtp) cc_final: 0.9229 (mtp) REVERT: D 155 MET cc_start: 0.8639 (tpt) cc_final: 0.8434 (tmm) REVERT: D 229 LEU cc_start: 0.9504 (mt) cc_final: 0.9073 (mt) REVERT: D 256 MET cc_start: 0.8201 (ttm) cc_final: 0.7732 (ttm) REVERT: D 373 MET cc_start: 0.8747 (mtp) cc_final: 0.8391 (ptp) REVERT: D 457 MET cc_start: 0.9297 (mtp) cc_final: 0.8916 (mmt) REVERT: D 581 MET cc_start: 0.8887 (pmm) cc_final: 0.8592 (pmm) REVERT: D 706 MET cc_start: 0.9171 (mmm) cc_final: 0.8895 (mmm) REVERT: D 1112 MET cc_start: 0.7715 (mmm) cc_final: 0.7163 (mmm) REVERT: E 42 GLU cc_start: 0.9538 (mt-10) cc_final: 0.8859 (tp30) REVERT: F 281 MET cc_start: 0.8966 (ptp) cc_final: 0.8632 (pmm) REVERT: F 282 MET cc_start: 0.9357 (mmm) cc_final: 0.8930 (mmm) REVERT: J 60 MET cc_start: 0.8421 (ppp) cc_final: 0.7154 (ppp) REVERT: J 69 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8385 (tm) REVERT: J 86 LEU cc_start: 0.9796 (OUTLIER) cc_final: 0.9573 (pp) REVERT: M 11 TYR cc_start: 0.9066 (t80) cc_final: 0.8326 (t80) REVERT: M 55 TYR cc_start: 0.8334 (m-80) cc_final: 0.7988 (m-80) outliers start: 56 outliers final: 42 residues processed: 165 average time/residue: 0.1796 time to fit residues: 49.3886 Evaluate side-chains 156 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 56 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026640 restraints weight = 252517.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027483 restraints weight = 137828.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.028059 restraints weight = 91875.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.028443 restraints weight = 69901.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.028682 restraints weight = 58098.221| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30549 Z= 0.145 Angle : 0.636 12.118 41912 Z= 0.328 Chirality : 0.043 0.385 4775 Planarity : 0.004 0.062 5070 Dihedral : 19.211 179.313 5207 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.82 % Allowed : 10.83 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3488 helix: 1.44 (0.14), residues: 1415 sheet: -0.86 (0.29), residues: 330 loop : -1.34 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 109 TYR 0.026 0.001 TYR E 67 PHE 0.016 0.001 PHE C 61 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (30542) covalent geometry : angle 0.63498 / 0.33 (41906) hydrogen bonds : bond 0.03882 / 2.64 ( 1363) hydrogen bonds : angle 4.51529 / 3.17 ( 3794) metal coordination : bond 0.00401 / 0.19 ( 7) metal coordination : angle 2.90437 / 1.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8963 (ttm) cc_final: 0.8674 (tmm) REVERT: B 1 MET cc_start: 0.8558 (tpp) cc_final: 0.7875 (tpp) REVERT: B 173 LYS cc_start: 0.9087 (tptp) cc_final: 0.8641 (tptp) REVERT: B 177 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8132 (ptmm) REVERT: B 191 LYS cc_start: 0.9243 (ttpt) cc_final: 0.8667 (tttp) REVERT: C 103 MET cc_start: 0.9262 (ptm) cc_final: 0.8691 (ppp) REVERT: C 159 MET cc_start: 0.9285 (tpp) cc_final: 0.8828 (mmm) REVERT: C 355 MET cc_start: 0.8837 (tmm) cc_final: 0.8634 (tmm) REVERT: C 393 MET cc_start: 0.9413 (tpp) cc_final: 0.9007 (tpp) REVERT: C 396 MET cc_start: 0.9444 (tmt) cc_final: 0.9154 (tmm) REVERT: C 404 MET cc_start: 0.8648 (ptp) cc_final: 0.8281 (ptp) REVERT: C 586 MET cc_start: 0.9289 (ppp) cc_final: 0.8305 (ppp) REVERT: C 607 MET cc_start: 0.8986 (mtt) cc_final: 0.8505 (mtm) REVERT: C 611 MET cc_start: 0.9188 (mtm) cc_final: 0.8756 (mtp) REVERT: C 661 MET cc_start: 0.8821 (tpt) cc_final: 0.8439 (tpt) REVERT: C 672 MET cc_start: 0.8820 (tpp) cc_final: 0.8489 (tpp) REVERT: C 784 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9018 (pp) REVERT: C 907 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9046 (tm) REVERT: C 926 MET cc_start: 0.9000 (tpp) cc_final: 0.8611 (tpp) REVERT: C 1051 MET cc_start: 0.9175 (tpt) cc_final: 0.8907 (tpp) REVERT: C 1076 MET cc_start: 0.9342 (mmm) cc_final: 0.8934 (mmm) REVERT: C 1119 GLU cc_start: 0.8671 (tp30) cc_final: 0.8318 (tp30) REVERT: D 143 MET cc_start: 0.9471 (mtp) cc_final: 0.9219 (mtp) REVERT: D 155 MET cc_start: 0.8626 (tpt) cc_final: 0.8423 (tmm) REVERT: D 229 LEU cc_start: 0.9478 (mt) cc_final: 0.9034 (mt) REVERT: D 256 MET cc_start: 0.8229 (ttm) cc_final: 0.7745 (ttm) REVERT: D 373 MET cc_start: 0.8729 (mtp) cc_final: 0.8368 (ptp) REVERT: D 457 MET cc_start: 0.9294 (mtp) cc_final: 0.8916 (mmt) REVERT: D 516 LEU cc_start: 0.9418 (mt) cc_final: 0.9076 (pt) REVERT: D 581 MET cc_start: 0.8895 (pmm) cc_final: 0.8603 (pmm) REVERT: D 975 CYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8721 (p) REVERT: D 1112 MET cc_start: 0.7775 (mmm) cc_final: 0.7514 (mmm) REVERT: E 42 GLU cc_start: 0.9532 (mt-10) cc_final: 0.8884 (tp30) REVERT: F 282 MET cc_start: 0.9355 (mmm) cc_final: 0.8988 (mmm) REVERT: J 60 MET cc_start: 0.8415 (ppp) cc_final: 0.7041 (ppp) REVERT: J 86 LEU cc_start: 0.9796 (OUTLIER) cc_final: 0.9572 (pp) REVERT: M 11 TYR cc_start: 0.9067 (t80) cc_final: 0.8297 (t80) REVERT: M 55 TYR cc_start: 0.8420 (m-80) cc_final: 0.8042 (m-80) outliers start: 53 outliers final: 44 residues processed: 155 average time/residue: 0.1805 time to fit residues: 46.7226 Evaluate side-chains 155 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 293 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 277 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.035903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.026459 restraints weight = 256100.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.027298 restraints weight = 141047.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027859 restraints weight = 94705.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.028245 restraints weight = 72195.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028477 restraints weight = 60107.441| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30549 Z= 0.175 Angle : 0.649 11.409 41912 Z= 0.334 Chirality : 0.043 0.387 4775 Planarity : 0.004 0.062 5070 Dihedral : 19.205 179.513 5207 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.71 % Allowed : 11.00 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3488 helix: 1.43 (0.14), residues: 1422 sheet: -0.74 (0.30), residues: 325 loop : -1.35 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 109 TYR 0.020 0.001 TYR E 56 PHE 0.016 0.001 PHE C 61 TRP 0.013 0.001 TRP J 82 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (30542) covalent geometry : angle 0.64770 / 0.33 (41906) hydrogen bonds : bond 0.04023 / 2.74 ( 1363) hydrogen bonds : angle 4.55768 / 3.20 ( 3794) metal coordination : bond 0.00616 / 0.31 ( 7) metal coordination : angle 2.84277 / 1.24 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4341.56 seconds wall clock time: 76 minutes 0.60 seconds (4560.60 seconds total)