Starting phenix.real_space_refine on Sat Aug 8 14:24:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e84_47706/08_2026/9e84_47706.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.047 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 86 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 17288 2.51 5 N 4987 2.21 5 O 5548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28008 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1700 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "B" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1695 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8484 Classifications: {'peptide': 1096} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1034} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9861 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1202} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 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: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1928 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 80} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1231 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 804 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "R" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12345 SG CYS D 60 77.030 31.982 58.556 1.00109.34 S ATOM 12363 SG CYS D 62 75.507 30.962 55.237 1.00114.78 S ATOM 12472 SG CYS D 75 79.187 31.481 55.417 1.00116.74 S ATOM 12498 SG CYS D 78 76.833 34.405 55.598 1.00109.64 S ATOM 18907 SG CYS D 891 108.428 69.949 103.302 1.00 75.83 S ATOM 19474 SG CYS D 968 104.803 70.043 102.995 1.00 71.34 S ATOM 19516 SG CYS D 975 106.393 67.716 105.305 1.00 69.10 S ATOM 19534 SG CYS D 978 106.422 71.314 106.057 1.00 67.14 S Time building chain proxies: 5.69, per 1000 atoms: 0.20 Number of scatterers: 28008 At special positions: 0 Unit cell: (131.272, 133.424, 187.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 96 16.00 P 86 15.00 Mg 1 11.99 O 5548 8.00 N 4987 7.00 C 17288 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: 2.46 Conformation dependent library (CDL) restraints added in 967.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " Number of angles added : 12 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6242 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 43 sheets defined 43.3% alpha, 15.3% beta 35 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.626A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.436A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.662A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.825A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.897A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.527A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.930A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (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 445 through 452 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.736A pdb=" N ARG C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 474' Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.916A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.430A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 777 through 781 removed outlier: 3.523A pdb=" N LEU C 781 " --> pdb=" O ASP C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.653A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.596A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.891A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.571A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.559A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 144 through 186 removed outlier: 3.691A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.273A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.526A pdb=" N SER D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.900A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.862A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 339 through 361 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 417 removed outlier: 3.517A pdb=" N GLN D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.459A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 4.066A pdb=" N LYS D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.352A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.852A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.654A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.678A 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 727 removed outlier: 3.806A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 removed outlier: 3.527A pdb=" N VAL D 736 " --> pdb=" O MET D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.873A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.918A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1126 Processing helix chain 'D' and resid 1126 through 1144 Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.210A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.798A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D1227 " --> pdb=" O ALA D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.779A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.670A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 221 removed outlier: 3.768A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.309A pdb=" N VAL F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.600A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.740A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.926A 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 404 removed outlier: 3.603A pdb=" N LEU F 399 " --> pdb=" O THR F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 418 Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.838A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 461 Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.793A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 110 removed outlier: 4.023A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 52 through 57 removed outlier: 3.511A pdb=" N GLY M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 98 Processing helix chain 'M' and resid 101 through 118 Processing helix chain 'M' and resid 122 through 144 removed outlier: 3.575A pdb=" N ARG M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.378A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.119A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 50 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.565A pdb=" N SER A 86 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 117 " --> pdb=" O SER A 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.770A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.615A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 8.058A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 141 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.623A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.544A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.536A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.749A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL M 48 " --> pdb=" O LEU M 35 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS M 32 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR M 24 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.771A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 192 removed outlier: 4.307A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.996A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 568 through 572 removed outlier: 3.617A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 667 through 671 removed outlier: 7.002A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 687 through 688 Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.593A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.449A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 8.175A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS C 876 " --> pdb=" O SER C 844 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N SER C 844 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.991A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 806 through 808 Processing sheet with id=AC9, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.298A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.334A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.801A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 422 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 4.094A pdb=" N GLU C1136 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C1138 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.365A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.684A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.900A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 392 through 393 removed outlier: 3.758A pdb=" N ARG D 397 " --> pdb=" O GLY D 393 " (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 822 through 825 removed outlier: 9.599A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 898 through 899 removed outlier: 4.305A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 923 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1053 through 1056 removed outlier: 3.920A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.534A pdb=" N GLU E 105 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 27 through 33 Processing sheet with id=AE7, first strand: chain 'J' and resid 53 through 55 1213 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9348 1.34 - 1.47: 6284 1.47 - 1.59: 12681 1.59 - 1.71: 164 1.71 - 1.84: 170 Bond restraints: 28647 Sorted by residual: bond pdb=" C VAL D1088 " pdb=" N PHE D1089 " ideal model delta sigma weight residual 1.332 1.507 -0.174 1.40e-02 5.10e+03 1.55e+02 bond pdb=" CB PRO J 51 " pdb=" CG PRO J 51 " ideal model delta sigma weight residual 1.492 1.714 -0.222 5.00e-02 4.00e+02 1.98e+01 bond pdb=" C1' DT T 53 " pdb=" N1 DT T 53 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C3' DG N 74 " pdb=" C2' DG N 74 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C1' DC T 8 " pdb=" N1 DC T 8 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.15e+01 ... (remaining 28642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 38964 3.66 - 7.33: 189 7.33 - 10.99: 6 10.99 - 14.65: 2 14.65 - 18.31: 1 Bond angle restraints: 39162 Sorted by residual: angle pdb=" CA PRO J 51 " pdb=" N PRO J 51 " pdb=" CD PRO J 51 " ideal model delta sigma weight residual 112.00 101.73 10.27 1.40e+00 5.10e-01 5.38e+01 angle pdb=" P1 POP C2000 " pdb=" O POP C2000 " pdb=" P2 POP C2000 " ideal model delta sigma weight residual 139.66 121.35 18.31 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C VAL D1088 " pdb=" N PHE D1089 " pdb=" CA PHE D1089 " ideal model delta sigma weight residual 121.54 110.09 11.45 1.91e+00 2.74e-01 3.59e+01 angle pdb=" CA PRO C 233 " pdb=" N PRO C 233 " pdb=" CD PRO C 233 " ideal model delta sigma weight residual 112.00 104.01 7.99 1.40e+00 5.10e-01 3.26e+01 angle pdb=" N PRO J 51 " pdb=" CD PRO J 51 " pdb=" CG PRO J 51 " ideal model delta sigma weight residual 103.20 95.16 8.04 1.50e+00 4.44e-01 2.87e+01 ... (remaining 39157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 16527 33.66 - 67.33: 757 67.33 - 100.99: 38 100.99 - 134.65: 2 134.65 - 168.31: 2 Dihedral angle restraints: 17326 sinusoidal: 7630 harmonic: 9696 Sorted by residual: dihedral pdb=" CA LYS C 229 " pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta harmonic sigma weight residual 180.00 149.92 30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA ILE J 50 " pdb=" C ILE J 50 " pdb=" N PRO J 51 " pdb=" CA PRO J 51 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASN C 444 " pdb=" C ASN C 444 " pdb=" N PRO C 445 " pdb=" CA PRO C 445 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 17323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3519 0.049 - 0.098: 658 0.098 - 0.147: 247 0.147 - 0.196: 35 0.196 - 0.244: 6 Chirality restraints: 4465 Sorted by residual: chirality pdb=" CA ILE J 50 " pdb=" N ILE J 50 " pdb=" C ILE J 50 " pdb=" CB ILE J 50 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DT T 19 " pdb=" C4' DT T 19 " pdb=" O3' DT T 19 " pdb=" C2' DT T 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL C 236 " pdb=" CA VAL C 236 " pdb=" CG1 VAL C 236 " pdb=" CG2 VAL C 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 4462 not shown) Planarity restraints: 4857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 232 " -0.078 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 233 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 50 " 0.075 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO J 51 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO J 51 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 51 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 438 " 0.016 2.00e-02 2.50e+03 2.20e-02 8.50e+00 pdb=" CG PHE F 438 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE F 438 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE F 438 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE F 438 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE F 438 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 438 " 0.007 2.00e-02 2.50e+03 ... (remaining 4854 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 28 2.20 - 2.88: 11065 2.88 - 3.55: 43034 3.55 - 4.23: 64796 4.23 - 4.90: 110437 Nonbonded interactions: 229360 Sorted by model distance: nonbonded pdb=" O3' A R 5 " pdb="MG MG R 101 " model vdw 1.529 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb=" O2' A R 5 " model vdw 1.947 3.040 nonbonded pdb=" O VAL F 448 " pdb=" OG SER F 452 " model vdw 1.962 3.040 nonbonded pdb=" OG SER C 525 " pdb=" OE1 GLU C 527 " model vdw 1.980 3.040 nonbonded pdb=" O GLN C 442 " pdb=" OG SER C 678 " model vdw 1.994 3.040 ... (remaining 229355 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 4 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and resid 4 through 224) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 31.660 Find NCS groups from input model: 0.240 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.005 0.222 28655 Z= 0.280 Angle : 0.759 18.315 39174 Z= 0.452 Chirality : 0.047 0.244 4465 Planarity : 0.007 0.112 4857 Dihedral : 17.596 168.313 11084 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.91 % Favored : 92.94 % Rotamer: Outliers : 0.25 % Allowed : 22.17 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3358 helix: 0.60 (0.14), residues: 1331 sheet: -1.22 (0.26), residues: 386 loop : -1.43 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 230 TYR 0.023 0.001 TYR M 89 PHE 0.048 0.002 PHE F 438 TRP 0.027 0.002 TRP M 85 HIS 0.016 0.002 HIS D 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.28 (28647) covalent geometry : angle 0.75950 / 0.45 (39162) hydrogen bonds : bond 0.14070 / 9.81 ( 1293) hydrogen bonds : angle 6.26538 / 4.45 ( 3611) metal coordination : bond 0.07717 / 4.28 ( 8) metal coordination : angle 0.03062 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 800 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8275 (ttmm) REVERT: B 79 ASN cc_start: 0.8336 (t0) cc_final: 0.8022 (t0) REVERT: B 90 ASP cc_start: 0.8318 (p0) cc_final: 0.7938 (p0) REVERT: B 120 ASN cc_start: 0.8121 (t0) cc_final: 0.7818 (t0) REVERT: C 190 THR cc_start: 0.8365 (m) cc_final: 0.8008 (p) REVERT: C 211 TRP cc_start: 0.8112 (m-90) cc_final: 0.7901 (m-10) REVERT: C 383 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7322 (tp30) REVERT: C 757 ILE cc_start: 0.8862 (tp) cc_final: 0.8472 (mm) REVERT: C 800 ASP cc_start: 0.6000 (m-30) cc_final: 0.5773 (m-30) REVERT: C 904 MET cc_start: 0.8699 (mtp) cc_final: 0.8455 (ttm) REVERT: C 986 GLN cc_start: 0.8174 (tp40) cc_final: 0.7732 (tp40) REVERT: D 155 MET cc_start: 0.8577 (mtp) cc_final: 0.6784 (ptp) REVERT: D 409 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7625 (mtpp) REVERT: D 465 HIS cc_start: 0.7719 (m-70) cc_final: 0.7247 (m-70) REVERT: D 581 MET cc_start: 0.8552 (mtm) cc_final: 0.8280 (mtm) REVERT: D 1113 GLU cc_start: 0.8053 (tt0) cc_final: 0.7699 (tm-30) REVERT: E 60 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7060 (tpt90) REVERT: E 63 GLN cc_start: 0.8094 (mm110) cc_final: 0.7815 (tp40) REVERT: F 226 ASP cc_start: 0.8149 (t0) cc_final: 0.7597 (t0) REVERT: F 388 GLN cc_start: 0.7535 (tp40) cc_final: 0.6880 (tp40) REVERT: M 35 LEU cc_start: 0.8730 (mp) cc_final: 0.8510 (mm) outliers start: 7 outliers final: 4 residues processed: 804 average time/residue: 0.2026 time to fit residues: 244.8127 Evaluate side-chains 640 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 636 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 767 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 124 HIS C 438 GLN C 841 HIS C 935 HIS C1034 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 540 GLN D 564 ASN F 299 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.205272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141713 restraints weight = 48335.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144530 restraints weight = 24152.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.144455 restraints weight = 16372.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.145112 restraints weight = 16454.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145449 restraints weight = 14560.037| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28655 Z= 0.232 Angle : 0.790 12.477 39174 Z= 0.411 Chirality : 0.048 0.327 4465 Planarity : 0.006 0.082 4857 Dihedral : 14.997 179.147 4659 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 3.52 % Allowed : 22.31 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.86 (0.14), residues: 3358 helix: 0.58 (0.14), residues: 1366 sheet: -0.87 (0.28), residues: 342 loop : -1.50 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 229 TYR 0.019 0.002 TYR B 96 PHE 0.025 0.002 PHE C 153 TRP 0.038 0.003 TRP D 223 HIS 0.010 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (28647) covalent geometry : angle 0.78526 / 0.41 (39162) hydrogen bonds : bond 0.05313 / 3.70 ( 1293) hydrogen bonds : angle 5.34807 / 3.83 ( 3611) metal coordination : bond 0.01281 / 0.60 ( 8) metal coordination : angle 5.19655 / 2.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 670 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8365 (ttpp) REVERT: A 191 LYS cc_start: 0.8442 (ttmm) cc_final: 0.7751 (ttpp) REVERT: B 90 ASP cc_start: 0.8549 (p0) cc_final: 0.8178 (p0) REVERT: B 120 ASN cc_start: 0.8758 (t0) cc_final: 0.8209 (t0) REVERT: B 177 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7904 (ttmm) REVERT: C 136 THR cc_start: 0.8946 (m) cc_final: 0.8586 (p) REVERT: C 211 TRP cc_start: 0.8244 (m-90) cc_final: 0.7293 (m-10) REVERT: C 225 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8069 (tpp80) REVERT: C 227 ASP cc_start: 0.8085 (t0) cc_final: 0.7826 (t0) REVERT: C 259 ARG cc_start: 0.8886 (ptp90) cc_final: 0.8615 (mtm-85) REVERT: C 383 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7301 (tp30) REVERT: C 386 GLN cc_start: 0.8622 (tt0) cc_final: 0.8160 (tt0) REVERT: C 435 GLN cc_start: 0.7835 (mm110) cc_final: 0.7627 (mm110) REVERT: C 745 ASP cc_start: 0.7383 (t70) cc_final: 0.7071 (t70) REVERT: C 757 ILE cc_start: 0.8514 (tp) cc_final: 0.8093 (mm) REVERT: C 986 GLN cc_start: 0.8546 (tp40) cc_final: 0.8270 (tp40) REVERT: C 1094 ASP cc_start: 0.9157 (t0) cc_final: 0.8632 (t0) REVERT: D 61 TYR cc_start: 0.7914 (t80) cc_final: 0.7465 (t80) REVERT: D 412 ARG cc_start: 0.8267 (tpp-160) cc_final: 0.7900 (tpp80) REVERT: D 474 ARG cc_start: 0.8470 (tmt170) cc_final: 0.7931 (ptt90) REVERT: D 475 MET cc_start: 0.8540 (mmt) cc_final: 0.7249 (mmt) REVERT: D 533 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8445 (t0) REVERT: D 581 MET cc_start: 0.8642 (mtm) cc_final: 0.8305 (mtm) REVERT: D 948 GLU cc_start: 0.8344 (mp0) cc_final: 0.8077 (mp0) REVERT: D 1113 GLU cc_start: 0.9190 (tt0) cc_final: 0.8448 (tm-30) REVERT: D 1279 ARG cc_start: 0.8546 (tpt90) cc_final: 0.8250 (tpm170) REVERT: E 97 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7991 (ttm170) REVERT: F 251 LYS cc_start: 0.9199 (mttt) cc_final: 0.8993 (ptpt) REVERT: F 280 ASP cc_start: 0.7797 (m-30) cc_final: 0.7573 (m-30) REVERT: F 281 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8894 (ppp) REVERT: F 334 LYS cc_start: 0.7997 (tppp) cc_final: 0.7628 (tppp) REVERT: F 388 GLN cc_start: 0.8414 (tp40) cc_final: 0.7732 (tp40) REVERT: F 458 ASP cc_start: 0.8840 (t70) cc_final: 0.8535 (m-30) REVERT: J 32 TYR cc_start: 0.6730 (m-80) cc_final: 0.6385 (m-10) REVERT: J 84 MET cc_start: 0.9137 (mmm) cc_final: 0.8780 (mmm) REVERT: M 32 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8211 (mmtm) REVERT: M 34 TYR cc_start: 0.9083 (m-80) cc_final: 0.8782 (m-80) REVERT: M 114 ARG cc_start: 0.7526 (mpt180) cc_final: 0.7224 (mpt180) REVERT: M 132 ARG cc_start: 0.8930 (tpt-90) cc_final: 0.8259 (tpt170) outliers start: 99 outliers final: 51 residues processed: 721 average time/residue: 0.2008 time to fit residues: 220.8371 Evaluate side-chains 644 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 591 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 103 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 210 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 266 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 545 ASN C 935 HIS C1034 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 ASN D 854 HIS ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN F 388 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.206326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142745 restraints weight = 48452.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144687 restraints weight = 25049.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147708 restraints weight = 16287.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.148173 restraints weight = 13468.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148492 restraints weight = 12909.740| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28655 Z= 0.174 Angle : 0.737 12.320 39174 Z= 0.382 Chirality : 0.046 0.300 4465 Planarity : 0.005 0.085 4857 Dihedral : 15.000 179.172 4654 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 3.94 % Allowed : 23.09 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.78 (0.14), residues: 3358 helix: 0.63 (0.14), residues: 1359 sheet: -0.90 (0.26), residues: 382 loop : -1.42 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 372 TYR 0.026 0.002 TYR E 78 PHE 0.018 0.002 PHE A 63 TRP 0.037 0.002 TRP F 350 HIS 0.011 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (28647) covalent geometry : angle 0.73321 / 0.38 (39162) hydrogen bonds : bond 0.04817 / 3.34 ( 1293) hydrogen bonds : angle 5.10461 / 3.66 ( 3611) metal coordination : bond 0.00845 / 0.41 ( 8) metal coordination : angle 4.44104 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 647 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8925 (tppp) cc_final: 0.8371 (tptp) REVERT: A 173 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8263 (ttmm) REVERT: A 189 PHE cc_start: 0.7969 (p90) cc_final: 0.7583 (p90) REVERT: B 38 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 90 ASP cc_start: 0.8529 (p0) cc_final: 0.8138 (p0) REVERT: B 96 TYR cc_start: 0.6974 (m-80) cc_final: 0.6743 (m-10) REVERT: B 120 ASN cc_start: 0.8833 (t0) cc_final: 0.8303 (t0) REVERT: B 173 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8164 (mttp) REVERT: B 177 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7929 (ttpp) REVERT: C 136 THR cc_start: 0.8870 (m) cc_final: 0.8555 (p) REVERT: C 159 MET cc_start: 0.8185 (mmm) cc_final: 0.7910 (mmm) REVERT: C 203 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8138 (tptt) REVERT: C 211 TRP cc_start: 0.8139 (m-90) cc_final: 0.7656 (m-10) REVERT: C 227 ASP cc_start: 0.8056 (t0) cc_final: 0.7717 (t0) REVERT: C 259 ARG cc_start: 0.8800 (ptp90) cc_final: 0.8264 (ptp-170) REVERT: C 383 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 386 GLN cc_start: 0.8537 (tt0) cc_final: 0.8088 (tt0) REVERT: C 412 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 435 GLN cc_start: 0.7693 (mm110) cc_final: 0.7439 (mm110) REVERT: C 513 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6754 (mt-10) REVERT: C 745 ASP cc_start: 0.7313 (t70) cc_final: 0.7058 (t70) REVERT: C 757 ILE cc_start: 0.8537 (tp) cc_final: 0.8121 (mm) REVERT: D 61 TYR cc_start: 0.7929 (t80) cc_final: 0.7565 (t80) REVERT: D 141 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: D 205 MET cc_start: 0.2314 (mmt) cc_final: 0.1992 (tpp) REVERT: D 474 ARG cc_start: 0.8367 (tmt170) cc_final: 0.8071 (tmt-80) REVERT: D 475 MET cc_start: 0.8493 (mmt) cc_final: 0.7383 (mmm) REVERT: D 533 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8195 (t0) REVERT: D 581 MET cc_start: 0.8630 (mtm) cc_final: 0.8267 (mtm) REVERT: D 810 ASN cc_start: 0.8267 (t0) cc_final: 0.7976 (t0) REVERT: D 1113 GLU cc_start: 0.9161 (tt0) cc_final: 0.8433 (tm-30) REVERT: D 1276 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8923 (mp0) REVERT: D 1279 ARG cc_start: 0.8535 (tpt90) cc_final: 0.8032 (tpm170) REVERT: E 97 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.8078 (ttm170) REVERT: F 292 LYS cc_start: 0.9375 (pttm) cc_final: 0.9156 (pttp) REVERT: F 388 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7623 (tp-100) REVERT: F 458 ASP cc_start: 0.8861 (t70) cc_final: 0.8556 (m-30) REVERT: J 84 MET cc_start: 0.9043 (mmm) cc_final: 0.8749 (mmm) REVERT: J 86 LEU cc_start: 0.9077 (mm) cc_final: 0.7957 (mm) REVERT: J 104 LEU cc_start: 0.7882 (tp) cc_final: 0.7675 (pp) REVERT: M 34 TYR cc_start: 0.9131 (m-80) cc_final: 0.8234 (m-80) REVERT: M 114 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7345 (mpt180) REVERT: M 132 ARG cc_start: 0.8911 (tpt-90) cc_final: 0.8403 (tpt90) outliers start: 111 outliers final: 67 residues processed: 715 average time/residue: 0.2078 time to fit residues: 227.3248 Evaluate side-chains 663 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 103 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 333 optimal weight: 8.9990 chunk 37 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 chunk 18 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 729 HIS C1034 HIS ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 942 GLN D1150 HIS ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.206012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.145521 restraints weight = 48227.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.145361 restraints weight = 25718.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146270 restraints weight = 17525.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147029 restraints weight = 17099.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147503 restraints weight = 14625.746| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28655 Z= 0.175 Angle : 0.726 12.984 39174 Z= 0.373 Chirality : 0.046 0.301 4465 Planarity : 0.005 0.086 4857 Dihedral : 14.984 179.932 4654 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 4.83 % Allowed : 23.23 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.74 (0.14), residues: 3358 helix: 0.61 (0.14), residues: 1364 sheet: -0.70 (0.26), residues: 379 loop : -1.40 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 144 TYR 0.026 0.002 TYR D 241 PHE 0.026 0.002 PHE C 153 TRP 0.037 0.002 TRP D 223 HIS 0.010 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (28647) covalent geometry : angle 0.72022 / 0.37 (39162) hydrogen bonds : bond 0.04557 / 3.16 ( 1293) hydrogen bonds : angle 5.00458 / 3.60 ( 3611) metal coordination : bond 0.00727 / 0.43 ( 8) metal coordination : angle 5.47209 / 2.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 633 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8915 (tppp) cc_final: 0.8402 (tptp) REVERT: A 173 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8293 (ttmm) REVERT: A 189 PHE cc_start: 0.7875 (p90) cc_final: 0.7256 (p90) REVERT: B 90 ASP cc_start: 0.8432 (p0) cc_final: 0.8034 (p0) REVERT: B 120 ASN cc_start: 0.8871 (t0) cc_final: 0.8343 (t0) REVERT: B 173 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (mmtt) REVERT: B 177 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7962 (ttpp) REVERT: C 30 ASN cc_start: 0.7923 (m-40) cc_final: 0.7653 (m-40) REVERT: C 136 THR cc_start: 0.8852 (m) cc_final: 0.8524 (p) REVERT: C 159 MET cc_start: 0.8256 (mmm) cc_final: 0.8029 (mmm) REVERT: C 203 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8068 (tptt) REVERT: C 227 ASP cc_start: 0.8131 (t0) cc_final: 0.7772 (t0) REVERT: C 259 ARG cc_start: 0.8740 (ptp90) cc_final: 0.8288 (ptp-170) REVERT: C 368 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: C 386 GLN cc_start: 0.8557 (tt0) cc_final: 0.8124 (tt0) REVERT: C 412 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7549 (mm) REVERT: C 415 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 435 GLN cc_start: 0.7760 (mm110) cc_final: 0.7530 (mm110) REVERT: C 513 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 745 ASP cc_start: 0.7338 (t70) cc_final: 0.7087 (t70) REVERT: C 757 ILE cc_start: 0.8526 (tp) cc_final: 0.8129 (mm) REVERT: C 986 GLN cc_start: 0.8730 (tp40) cc_final: 0.8320 (tp40) REVERT: D 61 TYR cc_start: 0.8089 (t80) cc_final: 0.7685 (t80) REVERT: D 134 TYR cc_start: 0.8340 (m-80) cc_final: 0.7316 (m-80) REVERT: D 141 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: D 155 MET cc_start: 0.8896 (mtp) cc_final: 0.8098 (mtm) REVERT: D 205 MET cc_start: 0.2294 (mmt) cc_final: 0.2070 (tpp) REVERT: D 241 TYR cc_start: 0.8882 (t80) cc_final: 0.7958 (t80) REVERT: D 242 ARG cc_start: 0.8979 (mmm160) cc_final: 0.8035 (mmm160) REVERT: D 330 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (tp) REVERT: D 342 ASP cc_start: 0.8406 (t70) cc_final: 0.7914 (t0) REVERT: D 353 ARG cc_start: 0.8424 (ttm170) cc_final: 0.8066 (ttm-80) REVERT: D 474 ARG cc_start: 0.8458 (tmt170) cc_final: 0.8139 (tmt-80) REVERT: D 475 MET cc_start: 0.8464 (mmt) cc_final: 0.7392 (mmm) REVERT: D 533 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8201 (t0) REVERT: D 581 MET cc_start: 0.8643 (mtm) cc_final: 0.8288 (mtm) REVERT: D 778 TRP cc_start: 0.9067 (m100) cc_final: 0.8839 (m100) REVERT: D 810 ASN cc_start: 0.8244 (t0) cc_final: 0.7962 (t0) REVERT: D 915 TYR cc_start: 0.8537 (m-10) cc_final: 0.6415 (m-10) REVERT: D 958 THR cc_start: 0.5867 (OUTLIER) cc_final: 0.5200 (t) REVERT: D 959 GLN cc_start: 0.8818 (pm20) cc_final: 0.8611 (tp-100) REVERT: D 1112 MET cc_start: 0.9260 (tpp) cc_final: 0.8980 (tpp) REVERT: D 1276 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8947 (mp0) REVERT: D 1279 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8057 (tpm170) REVERT: E 37 ASN cc_start: 0.7624 (t0) cc_final: 0.7417 (t0) REVERT: E 97 ARG cc_start: 0.8592 (ttp-170) cc_final: 0.8126 (ttm170) REVERT: F 258 TYR cc_start: 0.8540 (t80) cc_final: 0.8281 (t80) REVERT: F 334 LYS cc_start: 0.7704 (tppp) cc_final: 0.7485 (tppp) REVERT: F 359 MET cc_start: 0.8994 (tpp) cc_final: 0.8695 (mmm) REVERT: F 388 GLN cc_start: 0.8237 (tp40) cc_final: 0.7322 (tp40) REVERT: F 458 ASP cc_start: 0.8843 (t70) cc_final: 0.8577 (m-30) REVERT: J 84 MET cc_start: 0.8891 (mmm) cc_final: 0.8583 (mmm) REVERT: J 86 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8032 (mm) REVERT: M 34 TYR cc_start: 0.9094 (m-80) cc_final: 0.8226 (m-80) REVERT: M 132 ARG cc_start: 0.8916 (tpt-90) cc_final: 0.8716 (tpt90) outliers start: 136 outliers final: 78 residues processed: 716 average time/residue: 0.1897 time to fit residues: 209.5447 Evaluate side-chains 670 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 583 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 990 ASP Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 334 optimal weight: 50.0000 chunk 124 optimal weight: 0.3980 chunk 147 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 241 optimal weight: 0.0270 chunk 135 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 729 HIS ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 468 ASN D 942 GLN E 70 GLN E 88 GLN F 293 ASN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.207909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147139 restraints weight = 48207.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.147795 restraints weight = 25982.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.148731 restraints weight = 16988.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149363 restraints weight = 16318.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150506 restraints weight = 14354.346| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28655 Z= 0.146 Angle : 0.728 14.314 39174 Z= 0.371 Chirality : 0.046 0.299 4465 Planarity : 0.005 0.084 4857 Dihedral : 14.961 179.081 4654 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 4.19 % Allowed : 24.44 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.68 (0.14), residues: 3358 helix: 0.67 (0.14), residues: 1366 sheet: -0.77 (0.26), residues: 390 loop : -1.36 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 229 TYR 0.034 0.002 TYR M 89 PHE 0.033 0.002 PHE B 189 TRP 0.040 0.003 TRP D 223 HIS 0.012 0.001 HIS C 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (28647) covalent geometry : angle 0.72333 / 0.37 (39162) hydrogen bonds : bond 0.04291 / 2.98 ( 1293) hydrogen bonds : angle 4.85708 / 3.50 ( 3611) metal coordination : bond 0.00766 / 0.48 ( 8) metal coordination : angle 4.64097 / 2.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 631 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8822 (tppp) cc_final: 0.8427 (tptp) REVERT: A 173 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8261 (ttmm) REVERT: A 189 PHE cc_start: 0.7861 (p90) cc_final: 0.7245 (p90) REVERT: B 90 ASP cc_start: 0.8272 (p0) cc_final: 0.7877 (p0) REVERT: B 120 ASN cc_start: 0.8874 (t0) cc_final: 0.8361 (t0) REVERT: B 173 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8091 (mmtt) REVERT: C 30 ASN cc_start: 0.7813 (m-40) cc_final: 0.7584 (m-40) REVERT: C 103 MET cc_start: 0.7923 (tpp) cc_final: 0.7284 (tpp) REVERT: C 136 THR cc_start: 0.8782 (m) cc_final: 0.8456 (p) REVERT: C 159 MET cc_start: 0.8259 (mmm) cc_final: 0.7990 (mmm) REVERT: C 186 TYR cc_start: 0.7579 (m-80) cc_final: 0.7116 (m-10) REVERT: C 203 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7985 (tptt) REVERT: C 227 ASP cc_start: 0.8179 (t0) cc_final: 0.7801 (t0) REVERT: C 259 ARG cc_start: 0.8754 (ptp90) cc_final: 0.8254 (ptp-170) REVERT: C 305 ARG cc_start: 0.7199 (mtm180) cc_final: 0.6664 (mtm-85) REVERT: C 386 GLN cc_start: 0.8482 (tt0) cc_final: 0.8063 (tt0) REVERT: C 412 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7087 (mm) REVERT: C 415 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7768 (tm-30) REVERT: C 513 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6707 (mt-10) REVERT: C 620 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7061 (tmt-80) REVERT: C 745 ASP cc_start: 0.7266 (t70) cc_final: 0.6987 (t70) REVERT: C 757 ILE cc_start: 0.8608 (tp) cc_final: 0.8214 (mm) REVERT: D 61 TYR cc_start: 0.8049 (t80) cc_final: 0.7619 (t80) REVERT: D 134 TYR cc_start: 0.8220 (m-80) cc_final: 0.7936 (m-80) REVERT: D 223 TRP cc_start: 0.6746 (m100) cc_final: 0.6329 (m100) REVERT: D 330 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7605 (tp) REVERT: D 342 ASP cc_start: 0.8432 (t70) cc_final: 0.7987 (t0) REVERT: D 404 ASP cc_start: 0.8251 (m-30) cc_final: 0.7841 (m-30) REVERT: D 474 ARG cc_start: 0.8479 (tmt170) cc_final: 0.7637 (tmt-80) REVERT: D 475 MET cc_start: 0.8545 (mmt) cc_final: 0.7531 (mmm) REVERT: D 533 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8161 (t0) REVERT: D 581 MET cc_start: 0.8655 (mtm) cc_final: 0.8256 (mtm) REVERT: D 810 ASN cc_start: 0.8235 (t0) cc_final: 0.7937 (t0) REVERT: D 915 TYR cc_start: 0.8070 (m-10) cc_final: 0.7742 (m-80) REVERT: D 958 THR cc_start: 0.6231 (OUTLIER) cc_final: 0.5953 (t) REVERT: D 1140 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7045 (mp0) REVERT: D 1276 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8984 (mp0) REVERT: D 1279 ARG cc_start: 0.8594 (tpt90) cc_final: 0.8065 (tpm170) REVERT: E 37 ASN cc_start: 0.7620 (t0) cc_final: 0.7379 (t0) REVERT: E 97 ARG cc_start: 0.8609 (ttp-170) cc_final: 0.8243 (mtp180) REVERT: F 359 MET cc_start: 0.9035 (tpp) cc_final: 0.8810 (mmm) REVERT: F 372 MET cc_start: 0.9172 (mtp) cc_final: 0.8838 (ptp) REVERT: F 388 GLN cc_start: 0.8312 (tp40) cc_final: 0.7475 (tp40) REVERT: J 32 TYR cc_start: 0.6692 (m-80) cc_final: 0.6318 (m-80) REVERT: J 86 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8366 (mm) REVERT: M 34 TYR cc_start: 0.9160 (m-80) cc_final: 0.8260 (m-80) REVERT: M 85 TRP cc_start: 0.8749 (p-90) cc_final: 0.8335 (p-90) REVERT: M 132 ARG cc_start: 0.8914 (tpt-90) cc_final: 0.8437 (tpt90) outliers start: 118 outliers final: 62 residues processed: 703 average time/residue: 0.1915 time to fit residues: 209.9809 Evaluate side-chains 667 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 597 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 289 optimal weight: 10.0000 chunk 33 optimal weight: 0.0030 chunk 287 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 170 optimal weight: 50.0000 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN C 444 ASN C 451 HIS C 679 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.206132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144417 restraints weight = 48257.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145062 restraints weight = 25050.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145320 restraints weight = 16996.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145898 restraints weight = 17025.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146516 restraints weight = 14881.024| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28655 Z= 0.178 Angle : 0.731 13.764 39174 Z= 0.375 Chirality : 0.046 0.297 4465 Planarity : 0.005 0.081 4857 Dihedral : 14.956 178.653 4654 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 4.83 % Allowed : 24.30 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.73 (0.14), residues: 3358 helix: 0.62 (0.14), residues: 1368 sheet: -0.74 (0.26), residues: 384 loop : -1.39 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 356 TYR 0.023 0.002 TYR E 78 PHE 0.064 0.002 PHE F 438 TRP 0.037 0.002 TRP J 82 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (28647) covalent geometry : angle 0.72574 / 0.38 (39162) hydrogen bonds : bond 0.04313 / 3.00 ( 1293) hydrogen bonds : angle 4.83761 / 3.47 ( 3611) metal coordination : bond 0.00830 / 0.44 ( 8) metal coordination : angle 5.08820 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 614 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8823 (tppp) cc_final: 0.8413 (tptp) REVERT: A 173 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8285 (ttmm) REVERT: A 189 PHE cc_start: 0.7763 (p90) cc_final: 0.7027 (p90) REVERT: B 90 ASP cc_start: 0.8212 (p0) cc_final: 0.7823 (p0) REVERT: B 120 ASN cc_start: 0.8877 (t0) cc_final: 0.8339 (t0) REVERT: B 173 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (mmtt) REVERT: B 177 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7942 (ttpp) REVERT: C 30 ASN cc_start: 0.7866 (m-40) cc_final: 0.7605 (m-40) REVERT: C 103 MET cc_start: 0.7934 (tpp) cc_final: 0.7396 (tpp) REVERT: C 136 THR cc_start: 0.8807 (m) cc_final: 0.8487 (p) REVERT: C 159 MET cc_start: 0.8288 (mmm) cc_final: 0.8033 (mmm) REVERT: C 186 TYR cc_start: 0.7583 (m-80) cc_final: 0.7238 (m-10) REVERT: C 227 ASP cc_start: 0.8223 (t0) cc_final: 0.7823 (t0) REVERT: C 255 SER cc_start: 0.5749 (OUTLIER) cc_final: 0.4328 (p) REVERT: C 259 ARG cc_start: 0.8795 (ptp90) cc_final: 0.8303 (ptp-170) REVERT: C 305 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6679 (mtm180) REVERT: C 386 GLN cc_start: 0.8541 (tt0) cc_final: 0.8098 (tt0) REVERT: C 395 ARG cc_start: 0.8718 (ptp90) cc_final: 0.8501 (ptp90) REVERT: C 415 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7726 (tm-30) REVERT: C 435 GLN cc_start: 0.7715 (mm110) cc_final: 0.7427 (mm110) REVERT: C 513 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6740 (mt-10) REVERT: C 620 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7132 (tmt-80) REVERT: C 657 TYR cc_start: 0.7968 (p90) cc_final: 0.7764 (p90) REVERT: C 745 ASP cc_start: 0.7413 (t70) cc_final: 0.7149 (t70) REVERT: C 757 ILE cc_start: 0.8647 (tp) cc_final: 0.8259 (mm) REVERT: C 986 GLN cc_start: 0.8469 (tp40) cc_final: 0.8246 (tp40) REVERT: D 25 TYR cc_start: 0.7780 (m-80) cc_final: 0.7294 (m-10) REVERT: D 61 TYR cc_start: 0.8129 (t80) cc_final: 0.7692 (t80) REVERT: D 134 TYR cc_start: 0.8143 (m-80) cc_final: 0.7818 (m-80) REVERT: D 141 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: D 223 TRP cc_start: 0.6918 (m100) cc_final: 0.6592 (m100) REVERT: D 256 MET cc_start: 0.7168 (mmt) cc_final: 0.6936 (mmt) REVERT: D 273 GLU cc_start: 0.9085 (tp30) cc_final: 0.8217 (tp30) REVERT: D 330 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7706 (tp) REVERT: D 342 ASP cc_start: 0.8415 (t70) cc_final: 0.7891 (t0) REVERT: D 404 ASP cc_start: 0.8297 (m-30) cc_final: 0.7897 (m-30) REVERT: D 474 ARG cc_start: 0.8392 (tmt170) cc_final: 0.7968 (tmt-80) REVERT: D 475 MET cc_start: 0.8462 (mmt) cc_final: 0.7630 (mmt) REVERT: D 533 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8206 (t0) REVERT: D 581 MET cc_start: 0.8662 (mtm) cc_final: 0.8293 (mtm) REVERT: D 778 TRP cc_start: 0.9058 (m100) cc_final: 0.8804 (m100) REVERT: D 780 GLU cc_start: 0.8587 (pt0) cc_final: 0.8314 (pt0) REVERT: D 810 ASN cc_start: 0.8266 (t0) cc_final: 0.8021 (t0) REVERT: D 915 TYR cc_start: 0.8168 (m-10) cc_final: 0.7818 (m-80) REVERT: D 1140 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7202 (mt-10) REVERT: D 1279 ARG cc_start: 0.8584 (tpt90) cc_final: 0.8085 (tpm170) REVERT: E 37 ASN cc_start: 0.7644 (t0) cc_final: 0.7377 (t0) REVERT: E 46 ARG cc_start: 0.8446 (mpt180) cc_final: 0.8144 (mpt-90) REVERT: E 97 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8418 (ttm170) REVERT: F 217 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8906 (ptpp) REVERT: F 254 GLU cc_start: 0.8808 (pt0) cc_final: 0.8564 (pt0) REVERT: F 282 MET cc_start: 0.9328 (mmm) cc_final: 0.9026 (mmm) REVERT: F 337 TYR cc_start: 0.6974 (p90) cc_final: 0.6760 (p90) REVERT: F 350 TRP cc_start: 0.7214 (t-100) cc_final: 0.6930 (t-100) REVERT: F 359 MET cc_start: 0.8982 (tpp) cc_final: 0.8754 (mmm) REVERT: F 372 MET cc_start: 0.9173 (mtp) cc_final: 0.8940 (ptp) REVERT: F 388 GLN cc_start: 0.8318 (tp40) cc_final: 0.7461 (tp40) REVERT: J 32 TYR cc_start: 0.6614 (m-80) cc_final: 0.6252 (m-80) REVERT: J 40 PHE cc_start: 0.3248 (OUTLIER) cc_final: 0.2780 (m-80) REVERT: J 86 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8361 (mm) REVERT: M 34 TYR cc_start: 0.9055 (m-80) cc_final: 0.8228 (m-80) REVERT: M 112 TRP cc_start: 0.8624 (t-100) cc_final: 0.8385 (t-100) REVERT: M 132 ARG cc_start: 0.8900 (tpt-90) cc_final: 0.8414 (tpt90) outliers start: 136 outliers final: 83 residues processed: 695 average time/residue: 0.1947 time to fit residues: 209.7309 Evaluate side-chains 660 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 569 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 40 PHE Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 100 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 320 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN C 444 ASN C 679 ASN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.201997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137451 restraints weight = 48132.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139930 restraints weight = 25264.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140098 restraints weight = 16599.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141058 restraints weight = 16741.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141147 restraints weight = 14474.576| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28655 Z= 0.187 Angle : 0.749 13.965 39174 Z= 0.382 Chirality : 0.046 0.299 4465 Planarity : 0.005 0.078 4857 Dihedral : 14.950 178.183 4654 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 4.23 % Allowed : 25.72 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.75 (0.14), residues: 3358 helix: 0.65 (0.14), residues: 1362 sheet: -0.87 (0.25), residues: 395 loop : -1.40 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 182 TYR 0.021 0.002 TYR E 78 PHE 0.036 0.002 PHE B 189 TRP 0.044 0.002 TRP J 82 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (28647) covalent geometry : angle 0.74380 / 0.38 (39162) hydrogen bonds : bond 0.04252 / 2.96 ( 1293) hydrogen bonds : angle 4.82842 / 3.48 ( 3611) metal coordination : bond 0.00878 / 0.46 ( 8) metal coordination : angle 5.05375 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 602 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7706 (tp30) cc_final: 0.6629 (tp30) REVERT: A 70 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8591 (tttp) REVERT: A 99 LYS cc_start: 0.8812 (tppp) cc_final: 0.8468 (tptp) REVERT: A 173 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8294 (ttmm) REVERT: A 189 PHE cc_start: 0.7636 (p90) cc_final: 0.6871 (p90) REVERT: B 39 ARG cc_start: 0.8504 (tpt170) cc_final: 0.8302 (tpt-90) REVERT: B 90 ASP cc_start: 0.8215 (p0) cc_final: 0.7826 (p0) REVERT: B 120 ASN cc_start: 0.8899 (t0) cc_final: 0.8342 (t0) REVERT: B 173 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8176 (mttp) REVERT: B 177 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7964 (ttpp) REVERT: C 30 ASN cc_start: 0.7948 (m-40) cc_final: 0.7682 (m-40) REVERT: C 103 MET cc_start: 0.8090 (tpp) cc_final: 0.7879 (tpp) REVERT: C 203 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7264 (tptt) REVERT: C 213 GLU cc_start: 0.7975 (mp0) cc_final: 0.7140 (mp0) REVERT: C 227 ASP cc_start: 0.8298 (t0) cc_final: 0.7943 (t0) REVERT: C 255 SER cc_start: 0.5730 (OUTLIER) cc_final: 0.4305 (p) REVERT: C 259 ARG cc_start: 0.8799 (ptp90) cc_final: 0.8326 (ptp-170) REVERT: C 305 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6802 (mtm180) REVERT: C 386 GLN cc_start: 0.8558 (tt0) cc_final: 0.8140 (tt0) REVERT: C 415 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 513 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: C 620 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7147 (tmt-80) REVERT: C 745 ASP cc_start: 0.7449 (t70) cc_final: 0.7193 (t70) REVERT: C 757 ILE cc_start: 0.8667 (tp) cc_final: 0.8281 (mm) REVERT: C 1021 TYR cc_start: 0.8731 (m-80) cc_final: 0.8277 (m-10) REVERT: D 25 TYR cc_start: 0.7790 (m-80) cc_final: 0.7159 (m-10) REVERT: D 61 TYR cc_start: 0.8163 (t80) cc_final: 0.7694 (t80) REVERT: D 134 TYR cc_start: 0.8275 (m-80) cc_final: 0.8023 (m-80) REVERT: D 141 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: D 155 MET cc_start: 0.8616 (mtp) cc_final: 0.8370 (mtm) REVERT: D 205 MET cc_start: 0.1464 (mmm) cc_final: 0.0362 (mmm) REVERT: D 241 TYR cc_start: 0.8733 (t80) cc_final: 0.8192 (t80) REVERT: D 263 LYS cc_start: 0.9281 (tppt) cc_final: 0.8944 (tppt) REVERT: D 273 GLU cc_start: 0.9133 (tp30) cc_final: 0.8179 (tp30) REVERT: D 330 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7689 (tp) REVERT: D 342 ASP cc_start: 0.8481 (t70) cc_final: 0.7953 (t0) REVERT: D 404 ASP cc_start: 0.8349 (m-30) cc_final: 0.7900 (m-30) REVERT: D 474 ARG cc_start: 0.8366 (tmt170) cc_final: 0.7854 (tmt-80) REVERT: D 475 MET cc_start: 0.8429 (mmt) cc_final: 0.7608 (mmt) REVERT: D 533 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8178 (t0) REVERT: D 581 MET cc_start: 0.8680 (mtm) cc_final: 0.8319 (mtm) REVERT: D 688 MET cc_start: 0.7808 (mmp) cc_final: 0.7431 (mmp) REVERT: D 778 TRP cc_start: 0.9076 (m100) cc_final: 0.8818 (m100) REVERT: D 780 GLU cc_start: 0.8615 (pt0) cc_final: 0.8356 (pt0) REVERT: D 810 ASN cc_start: 0.8358 (t0) cc_final: 0.8101 (t0) REVERT: D 915 TYR cc_start: 0.8223 (m-10) cc_final: 0.7802 (m-80) REVERT: D 983 MET cc_start: 0.8272 (mmm) cc_final: 0.8054 (mmt) REVERT: D 1112 MET cc_start: 0.9401 (tpp) cc_final: 0.9043 (tpp) REVERT: D 1276 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8824 (mp0) REVERT: D 1279 ARG cc_start: 0.8484 (tpt90) cc_final: 0.7998 (tpm170) REVERT: E 37 ASN cc_start: 0.7663 (t0) cc_final: 0.7395 (t0) REVERT: E 97 ARG cc_start: 0.8635 (ttp-170) cc_final: 0.8408 (ttm170) REVERT: F 254 GLU cc_start: 0.8788 (pt0) cc_final: 0.8523 (pt0) REVERT: F 350 TRP cc_start: 0.7258 (t-100) cc_final: 0.6891 (t-100) REVERT: F 372 MET cc_start: 0.9231 (mtp) cc_final: 0.8939 (ptp) REVERT: F 388 GLN cc_start: 0.8383 (tp40) cc_final: 0.7679 (tp40) REVERT: J 32 TYR cc_start: 0.6634 (m-80) cc_final: 0.6248 (m-80) REVERT: J 40 PHE cc_start: 0.3376 (OUTLIER) cc_final: 0.2900 (m-80) REVERT: J 86 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8358 (mm) REVERT: M 34 TYR cc_start: 0.9102 (m-80) cc_final: 0.8283 (m-80) REVERT: M 75 ARG cc_start: 0.8128 (mpt180) cc_final: 0.7757 (mmt-90) REVERT: M 130 LYS cc_start: 0.8619 (ptpt) cc_final: 0.8361 (pttm) REVERT: M 132 ARG cc_start: 0.8861 (tpt-90) cc_final: 0.8509 (tpt90) outliers start: 119 outliers final: 84 residues processed: 669 average time/residue: 0.1932 time to fit residues: 200.2452 Evaluate side-chains 665 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 571 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 40 PHE Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 314 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 GLN D1150 HIS F 362 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.203050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136941 restraints weight = 48237.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141992 restraints weight = 24104.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141813 restraints weight = 15327.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142464 restraints weight = 15160.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142618 restraints weight = 14204.849| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28655 Z= 0.162 Angle : 0.760 14.935 39174 Z= 0.386 Chirality : 0.047 0.339 4465 Planarity : 0.005 0.078 4857 Dihedral : 14.956 178.002 4654 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 3.91 % Allowed : 26.79 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.68 (0.14), residues: 3358 helix: 0.66 (0.14), residues: 1348 sheet: -0.67 (0.26), residues: 379 loop : -1.35 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 403 TYR 0.029 0.002 TYR F 258 PHE 0.030 0.002 PHE C 153 TRP 0.052 0.003 TRP D 223 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (28647) covalent geometry : angle 0.75609 / 0.39 (39162) hydrogen bonds : bond 0.04193 / 2.91 ( 1293) hydrogen bonds : angle 4.80352 / 3.45 ( 3611) metal coordination : bond 0.00713 / 0.39 ( 8) metal coordination : angle 4.72671 / 2.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 605 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7687 (tp30) cc_final: 0.7316 (pt0) REVERT: A 70 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8508 (tttp) REVERT: A 99 LYS cc_start: 0.8782 (tppp) cc_final: 0.8394 (tptp) REVERT: A 123 MET cc_start: 0.7583 (tmm) cc_final: 0.7293 (mtm) REVERT: A 173 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8286 (ttmm) REVERT: B 39 ARG cc_start: 0.8536 (tpt170) cc_final: 0.8210 (tpt-90) REVERT: B 90 ASP cc_start: 0.8228 (p0) cc_final: 0.7820 (p0) REVERT: B 120 ASN cc_start: 0.8932 (t0) cc_final: 0.8378 (t0) REVERT: B 173 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: C 30 ASN cc_start: 0.7936 (m-40) cc_final: 0.7631 (m-40) REVERT: C 88 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 159 MET cc_start: 0.8493 (mmm) cc_final: 0.7937 (mmm) REVERT: C 213 GLU cc_start: 0.8043 (mp0) cc_final: 0.7297 (mp0) REVERT: C 227 ASP cc_start: 0.8267 (t0) cc_final: 0.7894 (t0) REVERT: C 255 SER cc_start: 0.6085 (OUTLIER) cc_final: 0.4918 (p) REVERT: C 259 ARG cc_start: 0.8847 (ptp90) cc_final: 0.8345 (ptp-170) REVERT: C 305 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6779 (mtm180) REVERT: C 347 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8177 (mmm-85) REVERT: C 386 GLN cc_start: 0.8499 (tt0) cc_final: 0.8067 (tt0) REVERT: C 513 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: C 745 ASP cc_start: 0.7357 (t70) cc_final: 0.7145 (t70) REVERT: C 918 ASN cc_start: 0.8104 (t0) cc_final: 0.7733 (t0) REVERT: C 1021 TYR cc_start: 0.8688 (m-80) cc_final: 0.8218 (m-10) REVERT: C 1136 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6451 (tm-30) REVERT: D 25 TYR cc_start: 0.7830 (m-80) cc_final: 0.6999 (m-10) REVERT: D 61 TYR cc_start: 0.8151 (t80) cc_final: 0.7747 (t80) REVERT: D 134 TYR cc_start: 0.8205 (m-80) cc_final: 0.7520 (m-80) REVERT: D 141 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: D 205 MET cc_start: 0.1981 (mmm) cc_final: 0.1534 (mmm) REVERT: D 223 TRP cc_start: 0.6910 (m100) cc_final: 0.6695 (m100) REVERT: D 263 LYS cc_start: 0.9290 (tppt) cc_final: 0.8963 (tppt) REVERT: D 273 GLU cc_start: 0.8885 (tp30) cc_final: 0.8209 (tp30) REVERT: D 330 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7751 (tp) REVERT: D 342 ASP cc_start: 0.8507 (t70) cc_final: 0.7962 (t0) REVERT: D 404 ASP cc_start: 0.8361 (m-30) cc_final: 0.7910 (m-30) REVERT: D 474 ARG cc_start: 0.8342 (tmt170) cc_final: 0.7941 (tmt-80) REVERT: D 475 MET cc_start: 0.8391 (mmt) cc_final: 0.7573 (mmt) REVERT: D 533 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8159 (t0) REVERT: D 581 MET cc_start: 0.8668 (mtm) cc_final: 0.8311 (mtm) REVERT: D 688 MET cc_start: 0.7764 (mmp) cc_final: 0.7402 (mmp) REVERT: D 780 GLU cc_start: 0.8627 (pt0) cc_final: 0.8356 (pt0) REVERT: D 810 ASN cc_start: 0.8341 (t0) cc_final: 0.8070 (t0) REVERT: D 915 TYR cc_start: 0.8184 (m-10) cc_final: 0.7735 (m-80) REVERT: D 983 MET cc_start: 0.8245 (mmm) cc_final: 0.8039 (mmt) REVERT: D 1276 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8884 (mp0) REVERT: D 1279 ARG cc_start: 0.8522 (tpt90) cc_final: 0.7989 (tpm170) REVERT: E 37 ASN cc_start: 0.7612 (t0) cc_final: 0.7331 (t0) REVERT: E 88 GLN cc_start: 0.7518 (mp10) cc_final: 0.7308 (pm20) REVERT: E 97 ARG cc_start: 0.8650 (ttp-170) cc_final: 0.8414 (ttm170) REVERT: F 249 LEU cc_start: 0.9509 (mm) cc_final: 0.9242 (mp) REVERT: F 282 MET cc_start: 0.9314 (mmm) cc_final: 0.9090 (mmm) REVERT: F 315 MET cc_start: 0.6523 (mpp) cc_final: 0.5937 (mmt) REVERT: F 350 TRP cc_start: 0.7294 (t-100) cc_final: 0.6877 (t-100) REVERT: F 362 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8767 (pp30) REVERT: F 372 MET cc_start: 0.9263 (mtp) cc_final: 0.8963 (ptp) REVERT: F 388 GLN cc_start: 0.8473 (tp40) cc_final: 0.7832 (tp40) REVERT: J 32 TYR cc_start: 0.6652 (m-80) cc_final: 0.6337 (m-80) REVERT: J 40 PHE cc_start: 0.3349 (OUTLIER) cc_final: 0.2893 (m-80) REVERT: J 86 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (mm) REVERT: M 34 TYR cc_start: 0.9130 (m-80) cc_final: 0.8323 (m-80) REVERT: M 95 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8662 (ptmt) outliers start: 110 outliers final: 83 residues processed: 672 average time/residue: 0.1820 time to fit residues: 193.0782 Evaluate side-chains 666 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 574 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 245 GLU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 362 GLN Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain J residue 40 PHE Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 295 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 252 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 314 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 HIS D1150 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.200767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134643 restraints weight = 48257.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136880 restraints weight = 24450.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138096 restraints weight = 16605.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138266 restraints weight = 15494.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138652 restraints weight = 14612.861| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28655 Z= 0.232 Angle : 0.795 14.584 39174 Z= 0.403 Chirality : 0.047 0.299 4465 Planarity : 0.006 0.075 4857 Dihedral : 14.980 178.900 4654 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.80 % Allowed : 27.07 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.74 (0.14), residues: 3358 helix: 0.65 (0.14), residues: 1343 sheet: -0.65 (0.27), residues: 371 loop : -1.43 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 159 TYR 0.023 0.002 TYR F 416 PHE 0.035 0.002 PHE B 189 TRP 0.077 0.004 TRP D 58 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (28647) covalent geometry : angle 0.78982 / 0.40 (39162) hydrogen bonds : bond 0.04303 / 2.99 ( 1293) hydrogen bonds : angle 4.88781 / 3.51 ( 3611) metal coordination : bond 0.01192 / 0.60 ( 8) metal coordination : angle 5.35777 / 2.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 590 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7756 (tp30) cc_final: 0.7378 (pt0) REVERT: A 70 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8492 (tttp) REVERT: A 99 LYS cc_start: 0.8814 (tppp) cc_final: 0.8416 (tptp) REVERT: A 123 MET cc_start: 0.7809 (tmm) cc_final: 0.7358 (mtm) REVERT: A 173 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8263 (ttpp) REVERT: B 39 ARG cc_start: 0.8496 (tpt170) cc_final: 0.8213 (tpt-90) REVERT: B 90 ASP cc_start: 0.8317 (p0) cc_final: 0.7900 (p0) REVERT: B 120 ASN cc_start: 0.8937 (t0) cc_final: 0.8375 (t0) REVERT: B 173 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8224 (mttp) REVERT: C 30 ASN cc_start: 0.7955 (m-40) cc_final: 0.7649 (m-40) REVERT: C 88 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 103 MET cc_start: 0.7930 (tpp) cc_final: 0.7538 (tpp) REVERT: C 159 MET cc_start: 0.8526 (mmm) cc_final: 0.8075 (mmm) REVERT: C 227 ASP cc_start: 0.8333 (t0) cc_final: 0.7979 (t0) REVERT: C 255 SER cc_start: 0.6626 (OUTLIER) cc_final: 0.5304 (p) REVERT: C 259 ARG cc_start: 0.8859 (ptp90) cc_final: 0.8463 (ptp-170) REVERT: C 305 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6722 (mtm180) REVERT: C 347 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8172 (mmm-85) REVERT: C 386 GLN cc_start: 0.8555 (tt0) cc_final: 0.8114 (tt0) REVERT: C 415 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 1021 TYR cc_start: 0.8723 (m-80) cc_final: 0.8237 (m-10) REVERT: C 1136 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6580 (tm-30) REVERT: D 25 TYR cc_start: 0.7813 (m-80) cc_final: 0.7583 (m-80) REVERT: D 29 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8637 (mmmm) REVERT: D 61 TYR cc_start: 0.8249 (t80) cc_final: 0.7777 (t80) REVERT: D 108 LYS cc_start: 0.8893 (tptp) cc_final: 0.8239 (tptp) REVERT: D 113 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8072 (mpt180) REVERT: D 134 TYR cc_start: 0.7901 (m-80) cc_final: 0.7684 (m-80) REVERT: D 141 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: D 205 MET cc_start: 0.1808 (mmm) cc_final: 0.1364 (mmm) REVERT: D 263 LYS cc_start: 0.9280 (tppt) cc_final: 0.8942 (tppt) REVERT: D 273 GLU cc_start: 0.8895 (tp30) cc_final: 0.8244 (tp30) REVERT: D 330 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7777 (tp) REVERT: D 342 ASP cc_start: 0.8450 (t70) cc_final: 0.7907 (t0) REVERT: D 344 TYR cc_start: 0.8737 (m-80) cc_final: 0.8470 (m-80) REVERT: D 404 ASP cc_start: 0.8367 (m-30) cc_final: 0.7941 (m-30) REVERT: D 474 ARG cc_start: 0.8325 (tmt170) cc_final: 0.7957 (tmt-80) REVERT: D 475 MET cc_start: 0.8429 (mmt) cc_final: 0.7591 (mmt) REVERT: D 533 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8175 (t0) REVERT: D 581 MET cc_start: 0.8659 (mtm) cc_final: 0.8326 (mtm) REVERT: D 688 MET cc_start: 0.7789 (mmp) cc_final: 0.7431 (mmp) REVERT: D 778 TRP cc_start: 0.9068 (m100) cc_final: 0.8861 (m100) REVERT: D 780 GLU cc_start: 0.8614 (pt0) cc_final: 0.8291 (pt0) REVERT: D 915 TYR cc_start: 0.8190 (m-10) cc_final: 0.7736 (m-80) REVERT: D 1276 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8918 (mp0) REVERT: D 1279 ARG cc_start: 0.8513 (tpt90) cc_final: 0.8210 (tpt90) REVERT: E 37 ASN cc_start: 0.7717 (t0) cc_final: 0.7449 (t0) REVERT: E 46 ARG cc_start: 0.8451 (mpt180) cc_final: 0.8091 (mpt-90) REVERT: E 97 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.8409 (ttm170) REVERT: F 221 LEU cc_start: 0.8891 (mt) cc_final: 0.8628 (pp) REVERT: F 282 MET cc_start: 0.9310 (mmm) cc_final: 0.9032 (mmm) REVERT: F 283 TRP cc_start: 0.9274 (t60) cc_final: 0.9061 (t60) REVERT: F 350 TRP cc_start: 0.7310 (t-100) cc_final: 0.6840 (t-100) REVERT: F 388 GLN cc_start: 0.8460 (tp40) cc_final: 0.7788 (tp40) REVERT: J 32 TYR cc_start: 0.6692 (m-80) cc_final: 0.6267 (m-80) REVERT: J 40 PHE cc_start: 0.3396 (OUTLIER) cc_final: 0.2879 (m-80) REVERT: M 34 TYR cc_start: 0.9142 (m-80) cc_final: 0.8340 (m-80) REVERT: M 95 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8511 (ptmt) outliers start: 107 outliers final: 89 residues processed: 656 average time/residue: 0.1979 time to fit residues: 202.1003 Evaluate side-chains 669 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 574 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1054 GLN Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 GLN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 245 GLU Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain J residue 40 PHE Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 3 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 282 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 272 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 285 optimal weight: 0.2980 chunk 104 optimal weight: 0.0980 chunk 283 optimal weight: 5.9990 chunk 337 optimal weight: 50.0000 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.203848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138325 restraints weight = 47780.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142533 restraints weight = 24583.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143965 restraints weight = 15418.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144448 restraints weight = 14683.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144537 restraints weight = 13335.826| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28655 Z= 0.154 Angle : 0.796 15.142 39174 Z= 0.403 Chirality : 0.047 0.319 4465 Planarity : 0.006 0.080 4857 Dihedral : 14.964 179.300 4652 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.82 % Rotamer: Outliers : 3.20 % Allowed : 27.99 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: -0.67 (0.14), residues: 3358 helix: 0.65 (0.14), residues: 1348 sheet: -0.63 (0.26), residues: 375 loop : -1.34 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 797 TYR 0.038 0.002 TYR C 314 PHE 0.038 0.002 PHE B 189 TRP 0.073 0.003 TRP J 82 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (28647) covalent geometry : angle 0.79226 / 0.40 (39162) hydrogen bonds : bond 0.04191 / 2.91 ( 1293) hydrogen bonds : angle 4.83384 / 3.47 ( 3611) metal coordination : bond 0.00451 / 0.26 ( 8) metal coordination : angle 4.66552 / 2.29 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 602 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7657 (tp30) cc_final: 0.7254 (pt0) REVERT: A 70 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8490 (tttp) REVERT: A 123 MET cc_start: 0.7767 (tmm) cc_final: 0.7365 (mtm) REVERT: A 173 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8274 (ttmm) REVERT: B 39 ARG cc_start: 0.8400 (tpt170) cc_final: 0.8157 (tpt-90) REVERT: B 90 ASP cc_start: 0.8317 (p0) cc_final: 0.7892 (p0) REVERT: B 120 ASN cc_start: 0.8938 (t0) cc_final: 0.8397 (t0) REVERT: B 173 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8153 (mttp) REVERT: B 177 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7935 (ttpp) REVERT: C 30 ASN cc_start: 0.7962 (m-40) cc_final: 0.7634 (m-40) REVERT: C 88 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 103 MET cc_start: 0.7915 (tpp) cc_final: 0.7543 (tpp) REVERT: C 159 MET cc_start: 0.8593 (mmm) cc_final: 0.8117 (mmm) REVERT: C 213 GLU cc_start: 0.7993 (mp0) cc_final: 0.6309 (tp30) REVERT: C 227 ASP cc_start: 0.8400 (t0) cc_final: 0.8028 (t0) REVERT: C 255 SER cc_start: 0.6494 (OUTLIER) cc_final: 0.5296 (p) REVERT: C 259 ARG cc_start: 0.8853 (ptp90) cc_final: 0.8408 (ptp-170) REVERT: C 305 ARG cc_start: 0.7371 (mtm180) cc_final: 0.6777 (mtm180) REVERT: C 347 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8218 (mmm-85) REVERT: C 383 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7624 (tm-30) REVERT: C 386 GLN cc_start: 0.8469 (tt0) cc_final: 0.8047 (tt0) REVERT: C 513 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6730 (mt-10) REVERT: C 1021 TYR cc_start: 0.8729 (m-80) cc_final: 0.8232 (m-10) REVERT: C 1136 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6424 (tm-30) REVERT: D 25 TYR cc_start: 0.7793 (m-80) cc_final: 0.7584 (m-80) REVERT: D 59 GLU cc_start: 0.7196 (pp20) cc_final: 0.6829 (pp20) REVERT: D 61 TYR cc_start: 0.8120 (t80) cc_final: 0.7662 (t80) REVERT: D 108 LYS cc_start: 0.8958 (tptp) cc_final: 0.8285 (tptp) REVERT: D 141 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: D 263 LYS cc_start: 0.9256 (tppt) cc_final: 0.8934 (tppt) REVERT: D 273 GLU cc_start: 0.8867 (tp30) cc_final: 0.8232 (tp30) REVERT: D 330 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7687 (tp) REVERT: D 342 ASP cc_start: 0.8470 (t70) cc_final: 0.7913 (t0) REVERT: D 404 ASP cc_start: 0.8288 (m-30) cc_final: 0.7835 (m-30) REVERT: D 474 ARG cc_start: 0.8318 (tmt170) cc_final: 0.7958 (tmt-80) REVERT: D 475 MET cc_start: 0.8396 (mmt) cc_final: 0.7572 (mmt) REVERT: D 533 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8131 (t0) REVERT: D 581 MET cc_start: 0.8660 (mtm) cc_final: 0.8286 (mtm) REVERT: D 688 MET cc_start: 0.7774 (mmp) cc_final: 0.7422 (mmp) REVERT: D 780 GLU cc_start: 0.8618 (pt0) cc_final: 0.8275 (pt0) REVERT: D 915 TYR cc_start: 0.8180 (m-10) cc_final: 0.7697 (m-80) REVERT: D 983 MET cc_start: 0.8203 (mmm) cc_final: 0.7968 (mmt) REVERT: D 1276 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8892 (mp0) REVERT: D 1279 ARG cc_start: 0.8468 (tpt90) cc_final: 0.7936 (tpm170) REVERT: E 37 ASN cc_start: 0.7640 (t0) cc_final: 0.7393 (t0) REVERT: E 97 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8267 (ttp-170) REVERT: F 221 LEU cc_start: 0.8888 (mt) cc_final: 0.8615 (pp) REVERT: F 282 MET cc_start: 0.9292 (mmm) cc_final: 0.8995 (mmm) REVERT: F 283 TRP cc_start: 0.9278 (t60) cc_final: 0.9060 (t60) REVERT: F 308 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8049 (tptt) REVERT: F 350 TRP cc_start: 0.7298 (t-100) cc_final: 0.6795 (t-100) REVERT: F 372 MET cc_start: 0.9182 (mtp) cc_final: 0.8836 (ptp) REVERT: F 388 GLN cc_start: 0.8441 (tp40) cc_final: 0.7833 (tp40) REVERT: J 31 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8717 (ttp80) REVERT: J 32 TYR cc_start: 0.6703 (m-80) cc_final: 0.6300 (m-80) REVERT: J 40 PHE cc_start: 0.3464 (OUTLIER) cc_final: 0.2848 (m-80) REVERT: M 34 TYR cc_start: 0.9113 (m-80) cc_final: 0.8333 (m-80) REVERT: M 95 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8754 (ptmm) outliers start: 90 outliers final: 72 residues processed: 657 average time/residue: 0.1869 time to fit residues: 191.8758 Evaluate side-chains 662 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 583 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1042 HIS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 946 ASP Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1154 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1222 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 40 PHE Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 71 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 204 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136941 restraints weight = 47866.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139248 restraints weight = 25566.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138635 restraints weight = 17294.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139720 restraints weight = 17178.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139814 restraints weight = 15046.107| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28655 Z= 0.214 Angle : 0.813 15.010 39174 Z= 0.411 Chirality : 0.048 0.385 4465 Planarity : 0.006 0.075 4857 Dihedral : 14.975 179.994 4652 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 3.13 % Allowed : 28.35 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.03 % 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: 3358 helix: 0.64 (0.14), residues: 1343 sheet: -0.62 (0.27), residues: 374 loop : -1.39 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 395 TYR 0.028 0.002 TYR D 241 PHE 0.046 0.002 PHE B 189 TRP 0.049 0.003 TRP D 223 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (28647) covalent geometry : angle 0.80791 / 0.41 (39162) hydrogen bonds : bond 0.04300 / 3.01 ( 1293) hydrogen bonds : angle 4.91739 / 3.52 ( 3611) metal coordination : bond 0.01057 / 0.54 ( 8) metal coordination : angle 5.21459 / 2.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.03 seconds wall clock time: 103 minutes 39.92 seconds (6219.92 seconds total)