Starting phenix.real_space_refine on Mon Jul 6 12:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji5_61497/07_2026/9ji5_61497.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 202 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 21004 2.51 5 N 6106 2.21 5 O 6959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34369 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 219} 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: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8554 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 9838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9838 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1202} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2105 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "G" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2047 Classifications: {'DNA': 100} Link IDs: {'rna3p': 99} Chain breaks: 1 Chain: "F" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: "M" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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: "K" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "I" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19055 SG CYS D 891 72.391 68.920 56.538 1.00 74.41 S ATOM 19622 SG CYS D 968 73.300 70.520 59.874 1.00 70.40 S ATOM 19664 SG CYS D 975 76.020 69.802 57.300 1.00 68.20 S ATOM 19682 SG CYS D 978 73.582 72.528 56.615 1.00 65.21 S ATOM 12509 SG CYS D 60 92.457 48.993 118.937 1.00114.89 S ATOM 12636 SG CYS D 75 89.109 45.907 119.171 1.00114.73 S ATOM 12662 SG CYS D 78 88.532 48.347 118.744 1.00112.24 S Time building chain proxies: 6.73, per 1000 atoms: 0.20 Number of scatterers: 34369 At special positions: 0 Unit cell: (248.4, 156, 162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 95 16.00 P 202 15.00 Mg 1 11.99 O 6959 8.00 N 6106 7.00 C 21004 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " Number of angles added : 6 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7160 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 53 sheets defined 43.5% alpha, 15.1% beta 80 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 4.401A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.542A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.061A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.952A 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: 4.116A 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 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.636A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.592A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.901A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' 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 613 removed outlier: 4.187A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.368A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 825 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 900 through 904 removed outlier: 3.826A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.270A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.533A 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 1079 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1095 through 1109 Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.605A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 185 Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.053A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.733A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.211A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.209A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.159A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.745A 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 560 through 564 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.574A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 652 Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'D' and resid 689 through 703 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.931A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (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 Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.716A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.821A 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 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.763A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1144 Proline residue: D1127 - end of helix removed outlier: 3.747A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.396A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.620A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.658A 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 101 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.192A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.065A pdb=" N ASP F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.747A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.850A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 3.906A pdb=" N VAL F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 removed outlier: 3.520A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.677A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.738A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 187 Processing helix chain 'J' and resid 195 through 202 Processing helix chain 'J' and resid 211 through 226 removed outlier: 4.043A pdb=" N GLU J 215 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 Processing helix chain 'M' and resid 195 through 202 Processing helix chain 'M' and resid 212 through 225 Processing helix chain 'O' and resid 175 through 187 Processing helix chain 'O' and resid 195 through 202 Processing helix chain 'O' and resid 211 through 226 removed outlier: 3.758A pdb=" N GLU O 215 " --> pdb=" O VAL O 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 195 through 203 Processing helix chain 'K' and resid 211 through 223 removed outlier: 4.201A pdb=" N GLU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 211 through 223 removed outlier: 4.376A pdb=" N GLU L 215 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG L 223 " --> pdb=" O SER L 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 188 removed outlier: 3.900A pdb=" N ASN N 188 " --> pdb=" O TYR N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 202 Processing helix chain 'N' and resid 211 through 225 removed outlier: 3.724A pdb=" N GLU N 215 " --> pdb=" O VAL N 211 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS N 224 " --> pdb=" O TYR N 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 255 Processing helix chain 'I' and resid 257 through 266 removed outlier: 3.904A pdb=" N TYR I 261 " --> pdb=" O THR I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 278 Processing helix chain 'I' and resid 279 through 285 Processing helix chain 'I' and resid 290 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.283A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.606A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.900A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.739A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.421A 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: 7.559A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (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: 6.342A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.691A 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 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.423A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.231A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.638A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.586A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 7.396A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.828A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.643A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.923A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.427A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.805A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 906 through 907 Processing sheet with id=AD2, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AD5, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.531A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.428A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.134A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.555A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.402A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1075 through 1077 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 Processing sheet with id=AE6, first strand: chain 'J' and resid 151 through 153 removed outlier: 3.613A pdb=" N ASP J 159 " --> pdb=" O GLU J 164 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU J 164 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL J 165 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 193 through 194 Processing sheet with id=AE8, first strand: chain 'M' and resid 151 through 153 removed outlier: 4.244A pdb=" N VAL M 165 " --> pdb=" O VAL M 172 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 193 through 194 Processing sheet with id=AF1, first strand: chain 'O' and resid 151 through 153 Processing sheet with id=AF2, first strand: chain 'O' and resid 193 through 194 Processing sheet with id=AF3, first strand: chain 'K' and resid 151 through 153 Processing sheet with id=AF4, first strand: chain 'K' and resid 193 through 194 Processing sheet with id=AF5, first strand: chain 'L' and resid 151 through 153 Processing sheet with id=AF6, first strand: chain 'L' and resid 193 through 194 Processing sheet with id=AF7, first strand: chain 'N' and resid 150 through 153 removed outlier: 4.448A pdb=" N VAL N 165 " --> pdb=" O VAL N 172 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 192 through 193 1452 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 207 hydrogen bonds 414 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 10.46 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5935 1.32 - 1.45: 9510 1.45 - 1.57: 19387 1.57 - 1.69: 401 1.69 - 1.81: 167 Bond restraints: 35400 Sorted by residual: bond pdb=" C5' DG H 98 " pdb=" C4' DG H 98 " ideal model delta sigma weight residual 1.512 1.481 0.031 7.00e-03 2.04e+04 1.96e+01 bond pdb=" C3' DG H 60 " pdb=" C2' DG H 60 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.59e+01 bond pdb=" C3' DG H 38 " pdb=" C2' DG H 38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG H 49 " pdb=" C2' DG H 49 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG G 72 " pdb=" C2' DG G 72 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 35395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 46650 1.73 - 3.47: 1962 3.47 - 5.20: 196 5.20 - 6.93: 30 6.93 - 8.67: 15 Bond angle restraints: 48853 Sorted by residual: angle pdb=" O4' DA H 15 " pdb=" C4' DA H 15 " pdb=" C3' DA H 15 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DG H 6 " pdb=" C4' DG H 6 " pdb=" C3' DG H 6 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT H 18 " pdb=" C4 DT H 18 " pdb=" O4 DT H 18 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4' DA H 92 " pdb=" C1' DA H 92 " pdb=" N9 DA H 92 " ideal model delta sigma weight residual 108.00 111.12 -3.12 7.00e-01 2.04e+00 1.99e+01 angle pdb=" O4 DT H 18 " pdb=" C4 DT H 18 " pdb=" C5 DT H 18 " ideal model delta sigma weight residual 124.90 121.82 3.08 7.00e-01 2.04e+00 1.94e+01 ... (remaining 48848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 19393 35.62 - 71.23: 1441 71.23 - 106.85: 54 106.85 - 142.46: 7 142.46 - 178.08: 12 Dihedral angle restraints: 20907 sinusoidal: 9772 harmonic: 11135 Sorted by residual: dihedral pdb=" CA VAL D 110 " pdb=" C VAL D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR J 152 " pdb=" C THR J 152 " pdb=" N PHE J 153 " pdb=" CA PHE J 153 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 20904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4749 0.067 - 0.134: 781 0.134 - 0.202: 46 0.202 - 0.269: 2 0.269 - 0.336: 4 Chirality restraints: 5582 Sorted by residual: chirality pdb=" P DG H 98 " pdb=" OP1 DG H 98 " pdb=" OP2 DG H 98 " pdb=" O5' DG H 98 " both_signs ideal model delta sigma weight residual True 2.34 -2.67 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL D1067 " pdb=" CA VAL D1067 " pdb=" CG1 VAL D1067 " pdb=" CG2 VAL D1067 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU M 221 " pdb=" CB LEU M 221 " pdb=" CD1 LEU M 221 " pdb=" CD2 LEU M 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 5579 not shown) Planarity restraints: 5648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 217 " 0.022 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR M 217 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR M 217 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR M 217 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR M 217 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR M 217 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 217 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 217 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 793 " -0.032 2.00e-02 2.50e+03 1.98e-02 7.83e+00 pdb=" CG TYR D 793 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 793 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 793 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR D 793 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 793 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR D 793 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 793 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 516 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO F 517 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 517 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 517 " 0.036 5.00e-02 4.00e+02 ... (remaining 5645 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 356 2.55 - 3.14: 27545 3.14 - 3.72: 58615 3.72 - 4.31: 75531 4.31 - 4.90: 121524 Nonbonded interactions: 283571 Sorted by model distance: nonbonded pdb=" O TRP K 166 " pdb=" NZ LYS K 167 " model vdw 1.960 3.120 nonbonded pdb=" OD1 ASP J 210 " pdb=" N VAL J 211 " model vdw 2.061 3.120 nonbonded pdb=" NH2 ARG D 77 " pdb="ZN ZN D2001 " model vdw 2.097 2.310 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D2002 " model vdw 2.125 2.170 nonbonded pdb=" OD1 ASP A 90 " pdb=" N GLU A 91 " model vdw 2.186 3.120 ... (remaining 283566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and (resid 2 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 226)) } ncs_group { reference = (chain 'J' and (resid 149 through 184 or (resid 185 and (name N or name CA or na \ me C or name O or name CB )) or resid 186 through 214 or (resid 215 and (name N \ or name CA or name C or name O or name CB )) or resid 216 through 244)) selection = (chain 'K' and (resid 149 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 214 or (resid \ 215 and (name N or name CA or name C or name O or name CB )) or resid 216 throug \ h 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or \ resid 238 through 244)) selection = (chain 'L' and (resid 149 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 214 or (resid 215 and (name N \ or name CA or name C or name O or name CB )) or resid 216 through 236 or (resid \ 237 and (name N or name CA or name C or name O or name CB )) or resid 238 throug \ h 244)) selection = (chain 'M' and (resid 149 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 244)) selection = (chain 'N' and (resid 149 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 214 or (resid \ 215 and (name N or name CA or name C or name O or name CB )) or resid 216 throug \ h 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or \ resid 238 through 244)) selection = (chain 'O' and (resid 149 through 184 or (resid 185 and (name N or name CA or na \ me C or name O or name CB )) or resid 186 through 214 or (resid 215 and (name N \ or name CA or name C or name O or name CB )) or resid 216 through 244)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 41.440 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 0.093 35407 Z= 0.332 Angle : 0.756 8.666 48859 Z= 0.509 Chirality : 0.048 0.336 5582 Planarity : 0.005 0.065 5648 Dihedral : 21.704 178.076 13747 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 0.40 % Allowed : 30.30 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.50 (0.13), residues: 3850 helix: 0.57 (0.13), residues: 1548 sheet: -0.21 (0.28), residues: 358 loop : -1.09 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 40 TYR 0.051 0.002 TYR M 217 PHE 0.021 0.002 PHE D 455 TRP 0.027 0.002 TRP M 203 HIS 0.006 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.33 (35400) covalent geometry : angle 0.75573 / 0.51 (48853) hydrogen bonds : bond 0.09227 / 6.39 ( 1651) hydrogen bonds : angle 5.45430 / 3.84 ( 4452) metal coordination : bond 0.00270 / 0.13 ( 7) metal coordination : angle 1.52523 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 321 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ILE cc_start: 0.7672 (tt) cc_final: 0.7030 (mm) REVERT: C 474 ASP cc_start: 0.8194 (m-30) cc_final: 0.7660 (m-30) REVERT: C 926 MET cc_start: 0.8371 (mmm) cc_final: 0.7923 (mmm) REVERT: F 297 GLU cc_start: 0.8041 (mp0) cc_final: 0.7775 (mp0) REVERT: F 502 ARG cc_start: 0.8066 (mmp-170) cc_final: 0.7547 (mmm160) REVERT: J 215 GLU cc_start: 0.8356 (tt0) cc_final: 0.8081 (mm-30) REVERT: K 183 ARG cc_start: 0.8328 (ptt90) cc_final: 0.7916 (ptm160) outliers start: 13 outliers final: 6 residues processed: 331 average time/residue: 0.2210 time to fit residues: 119.3474 Evaluate side-chains 276 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain N residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 ASN C 442 GLN C 775 ASN C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 767 HIS D1251 ASN E 70 GLN F 434 GLN M 212 ASN O 170 GLN O 188 ASN ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074942 restraints weight = 87488.274| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.98 r_work: 0.3043 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 35407 Z= 0.253 Angle : 0.716 11.090 48859 Z= 0.384 Chirality : 0.048 0.263 5582 Planarity : 0.005 0.058 5648 Dihedral : 22.246 175.709 6451 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.81 % Rotamer: Outliers : 4.93 % Allowed : 25.92 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.42 (0.13), residues: 3850 helix: 0.65 (0.13), residues: 1573 sheet: -0.19 (0.28), residues: 337 loop : -1.06 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 223 TYR 0.046 0.002 TYR M 217 PHE 0.020 0.002 PHE B 189 TRP 0.019 0.002 TRP M 203 HIS 0.023 0.001 HIS K 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (35400) covalent geometry : angle 0.71604 / 0.38 (48853) hydrogen bonds : bond 0.05483 / 3.82 ( 1651) hydrogen bonds : angle 4.92235 / 3.50 ( 4452) metal coordination : bond 0.01359 / 0.69 ( 7) metal coordination : angle 1.26955 / 0.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 264 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ILE cc_start: 0.7971 (tt) cc_final: 0.7412 (mm) REVERT: B 5 GLN cc_start: 0.8666 (tt0) cc_final: 0.8370 (tt0) REVERT: B 75 GLU cc_start: 0.8877 (mp0) cc_final: 0.8608 (tt0) REVERT: B 79 ASN cc_start: 0.9265 (m-40) cc_final: 0.9044 (m-40) REVERT: B 189 PHE cc_start: 0.8040 (m-80) cc_final: 0.7549 (m-80) REVERT: C 474 ASP cc_start: 0.8611 (m-30) cc_final: 0.8033 (m-30) REVERT: C 569 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: C 673 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7895 (ptm160) REVERT: C 926 MET cc_start: 0.8935 (mmm) cc_final: 0.8680 (mmm) REVERT: C 1005 ASP cc_start: 0.8869 (p0) cc_final: 0.8608 (p0) REVERT: D 126 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: D 450 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8846 (mm-30) REVERT: D 451 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9353 (mp) REVERT: D 474 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7626 (mtm110) REVERT: D 944 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8972 (tt) REVERT: D 963 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6755 (mtp180) REVERT: D 1244 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9083 (mptt) REVERT: E 46 ARG cc_start: 0.8809 (mtt90) cc_final: 0.8563 (mtt90) REVERT: E 70 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6997 (pp30) REVERT: F 297 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: F 427 ILE cc_start: 0.8645 (tp) cc_final: 0.8444 (tp) REVERT: F 502 ARG cc_start: 0.8265 (mmp-170) cc_final: 0.7636 (mmm160) REVERT: J 210 ASP cc_start: 0.8302 (t0) cc_final: 0.8077 (t0) REVERT: O 173 SER cc_start: 0.2186 (OUTLIER) cc_final: 0.1961 (m) REVERT: O 215 GLU cc_start: -0.0007 (OUTLIER) cc_final: -0.1188 (pp20) REVERT: O 217 TYR cc_start: 0.3481 (OUTLIER) cc_final: 0.3042 (t80) REVERT: K 162 THR cc_start: 0.5637 (OUTLIER) cc_final: 0.4871 (p) REVERT: K 167 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7266 (mtpt) REVERT: K 183 ARG cc_start: 0.8356 (ptt90) cc_final: 0.7906 (ptm160) REVERT: L 215 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5873 (pm20) outliers start: 160 outliers final: 72 residues processed: 408 average time/residue: 0.2071 time to fit residues: 139.8625 Evaluate side-chains 336 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 250 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1244 LYS Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 227 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 367 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 308 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 305 optimal weight: 40.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN C 775 ASN ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN M 163 HIS M 212 ASN ** N 170 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 = 0.3922 r_free = 0.3922 target = 0.114727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072752 restraints weight = 87746.522| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.07 r_work: 0.2985 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 35407 Z= 0.294 Angle : 0.727 9.697 48859 Z= 0.388 Chirality : 0.048 0.281 5582 Planarity : 0.005 0.061 5648 Dihedral : 22.211 174.514 6447 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 7.15 % Allowed : 24.48 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 3850 helix: 0.55 (0.13), residues: 1578 sheet: -0.31 (0.28), residues: 332 loop : -1.08 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 46 TYR 0.019 0.002 TYR J 184 PHE 0.031 0.002 PHE K 179 TRP 0.022 0.002 TRP M 203 HIS 0.011 0.001 HIS K 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.29 (35400) covalent geometry : angle 0.72665 / 0.39 (48853) hydrogen bonds : bond 0.05602 / 3.92 ( 1651) hydrogen bonds : angle 4.95158 / 3.52 ( 4452) metal coordination : bond 0.01342 / 0.68 ( 7) metal coordination : angle 1.25167 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 262 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3066 (OUTLIER) cc_final: 0.2790 (ttt) REVERT: B 75 GLU cc_start: 0.8999 (mp0) cc_final: 0.8640 (tt0) REVERT: B 79 ASN cc_start: 0.9245 (m-40) cc_final: 0.8990 (m-40) REVERT: B 179 ASP cc_start: 0.8212 (t0) cc_final: 0.7816 (t70) REVERT: C 232 GLN cc_start: 0.8077 (mp10) cc_final: 0.7565 (mp10) REVERT: C 467 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7944 (tpp80) REVERT: C 474 ASP cc_start: 0.8625 (m-30) cc_final: 0.8038 (m-30) REVERT: C 667 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8447 (ptp-110) REVERT: D 143 MET cc_start: 0.8574 (tmm) cc_final: 0.8350 (tmm) REVERT: D 259 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8915 (pm20) REVERT: D 435 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.8893 (pp30) REVERT: D 450 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8825 (mm-30) REVERT: D 451 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9184 (mp) REVERT: D 845 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8381 (p) REVERT: D 944 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8975 (tt) REVERT: E 41 ASP cc_start: 0.8795 (p0) cc_final: 0.8592 (p0) REVERT: E 70 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6704 (pp30) REVERT: E 73 GLU cc_start: 0.5196 (mp0) cc_final: 0.4958 (mp0) REVERT: F 297 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8791 (mp0) REVERT: F 427 ILE cc_start: 0.8848 (tp) cc_final: 0.8614 (tp) REVERT: F 502 ARG cc_start: 0.8278 (mmp-170) cc_final: 0.7612 (mmm160) REVERT: J 159 ASP cc_start: 0.8730 (t0) cc_final: 0.8486 (t0) REVERT: J 164 GLU cc_start: 0.8726 (pm20) cc_final: 0.8473 (pm20) REVERT: J 210 ASP cc_start: 0.8491 (t0) cc_final: 0.8226 (t0) REVERT: J 215 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8495 (mm-30) REVERT: O 217 TYR cc_start: 0.3456 (OUTLIER) cc_final: 0.3008 (t80) REVERT: K 160 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8322 (tm-30) REVERT: K 183 ARG cc_start: 0.8339 (ptt90) cc_final: 0.7939 (ptm160) REVERT: L 215 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5961 (pm20) REVERT: I 251 ILE cc_start: 0.2424 (OUTLIER) cc_final: 0.2003 (mt) outliers start: 232 outliers final: 126 residues processed: 466 average time/residue: 0.2019 time to fit residues: 157.9275 Evaluate side-chains 387 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 248 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 263 CYS Chi-restraints excluded: chain I residue 287 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 372 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 360 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 378 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 380 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN N 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.117089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075879 restraints weight = 88045.487| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.36 r_work: 0.3023 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35407 Z= 0.152 Angle : 0.641 9.010 48859 Z= 0.345 Chirality : 0.046 0.304 5582 Planarity : 0.004 0.059 5648 Dihedral : 22.143 176.185 6447 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.39 % Allowed : 26.26 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.27 (0.13), residues: 3850 helix: 0.80 (0.13), residues: 1567 sheet: -0.16 (0.29), residues: 323 loop : -0.99 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 91 TYR 0.022 0.001 TYR J 184 PHE 0.021 0.001 PHE K 179 TRP 0.015 0.001 TRP L 166 HIS 0.007 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (35400) covalent geometry : angle 0.64054 / 0.35 (48853) hydrogen bonds : bond 0.04881 / 3.41 ( 1651) hydrogen bonds : angle 4.73700 / 3.37 ( 4452) metal coordination : bond 0.00322 / 0.15 ( 7) metal coordination : angle 0.93872 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 269 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.8999 (mp0) cc_final: 0.8692 (tt0) REVERT: B 79 ASN cc_start: 0.9240 (m-40) cc_final: 0.8987 (m-40) REVERT: B 179 ASP cc_start: 0.8145 (t0) cc_final: 0.7720 (t70) REVERT: C 232 GLN cc_start: 0.8061 (mp10) cc_final: 0.7550 (mp10) REVERT: C 238 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8388 (mm) REVERT: C 467 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7816 (tpp80) REVERT: C 673 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7706 (ptm160) REVERT: C 1005 ASP cc_start: 0.8824 (p0) cc_final: 0.8500 (p0) REVERT: D 259 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8868 (pm20) REVERT: D 435 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.8878 (pp30) REVERT: D 450 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8768 (mm-30) REVERT: D 882 GLN cc_start: 0.8918 (pt0) cc_final: 0.8435 (pp30) REVERT: E 41 ASP cc_start: 0.8774 (p0) cc_final: 0.8554 (p0) REVERT: F 403 MET cc_start: 0.8582 (mmm) cc_final: 0.8360 (mmm) REVERT: F 427 ILE cc_start: 0.8820 (tp) cc_final: 0.8567 (tp) REVERT: F 502 ARG cc_start: 0.8258 (mmp-170) cc_final: 0.7618 (mmm160) REVERT: J 159 ASP cc_start: 0.8800 (t0) cc_final: 0.8451 (t0) REVERT: J 164 GLU cc_start: 0.8716 (pm20) cc_final: 0.8425 (pm20) REVERT: J 210 ASP cc_start: 0.8477 (t0) cc_final: 0.8212 (t0) REVERT: J 215 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: O 217 TYR cc_start: 0.3384 (OUTLIER) cc_final: 0.2966 (t80) REVERT: K 160 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8270 (tm-30) REVERT: K 183 ARG cc_start: 0.8351 (ptt90) cc_final: 0.7928 (ptm160) REVERT: L 215 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: I 270 HIS cc_start: 0.5515 (OUTLIER) cc_final: 0.5315 (m90) outliers start: 175 outliers final: 106 residues processed: 422 average time/residue: 0.1940 time to fit residues: 138.4070 Evaluate side-chains 365 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 251 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 172 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain I residue 270 HIS Chi-restraints excluded: chain I residue 288 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 66 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 345 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 257 optimal weight: 0.0970 chunk 163 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 349 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 813 GLN M 212 ASN ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075887 restraints weight = 87562.440| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.36 r_work: 0.3021 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35407 Z= 0.158 Angle : 0.634 8.957 48859 Z= 0.339 Chirality : 0.045 0.323 5582 Planarity : 0.004 0.059 5648 Dihedral : 22.092 175.977 6445 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.95 % Allowed : 26.14 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.16 (0.14), residues: 3850 helix: 0.94 (0.13), residues: 1561 sheet: -0.06 (0.29), residues: 320 loop : -0.97 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 762 TYR 0.022 0.001 TYR J 184 PHE 0.018 0.001 PHE K 179 TRP 0.014 0.001 TRP L 166 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (35400) covalent geometry : angle 0.63412 / 0.34 (48853) hydrogen bonds : bond 0.04709 / 3.27 ( 1651) hydrogen bonds : angle 4.66845 / 3.31 ( 4452) metal coordination : bond 0.00513 / 0.25 ( 7) metal coordination : angle 0.71998 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 263 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2016 (mmm) REVERT: B 5 GLN cc_start: 0.8658 (tt0) cc_final: 0.8420 (tt0) REVERT: B 75 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: B 79 ASN cc_start: 0.9245 (m-40) cc_final: 0.9024 (m-40) REVERT: B 179 ASP cc_start: 0.8238 (t0) cc_final: 0.7844 (t70) REVERT: C 232 GLN cc_start: 0.8119 (mp10) cc_final: 0.7608 (mp10) REVERT: C 238 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8403 (mm) REVERT: C 467 ARG cc_start: 0.8261 (tpp80) cc_final: 0.8049 (tpp80) REVERT: C 667 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8864 (ptp-110) REVERT: C 673 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7912 (ptm160) REVERT: C 767 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8586 (pt0) REVERT: C 1005 ASP cc_start: 0.8839 (p0) cc_final: 0.8522 (p0) REVERT: D 143 MET cc_start: 0.8540 (tmm) cc_final: 0.8317 (tmm) REVERT: D 259 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: D 435 GLN cc_start: 0.9469 (OUTLIER) cc_final: 0.8884 (pp30) REVERT: D 450 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8953 (tp30) REVERT: D 451 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9205 (mp) REVERT: D 497 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8661 (pp) REVERT: D 882 GLN cc_start: 0.8904 (pt0) cc_final: 0.8468 (pp30) REVERT: E 41 ASP cc_start: 0.8748 (p0) cc_final: 0.8522 (p0) REVERT: F 403 MET cc_start: 0.8596 (mmm) cc_final: 0.8323 (mmm) REVERT: F 427 ILE cc_start: 0.8847 (tp) cc_final: 0.8592 (tp) REVERT: F 502 ARG cc_start: 0.8270 (mmp-170) cc_final: 0.7721 (mmm160) REVERT: J 159 ASP cc_start: 0.8850 (t0) cc_final: 0.8430 (t0) REVERT: J 164 GLU cc_start: 0.8727 (pm20) cc_final: 0.8394 (pm20) REVERT: J 210 ASP cc_start: 0.8497 (t0) cc_final: 0.8233 (t0) REVERT: O 217 TYR cc_start: 0.3402 (OUTLIER) cc_final: 0.2922 (t80) REVERT: K 167 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7486 (mtpt) REVERT: K 183 ARG cc_start: 0.8352 (ptt90) cc_final: 0.7905 (ptm160) REVERT: K 213 VAL cc_start: 0.9197 (m) cc_final: 0.8817 (p) REVERT: K 217 TYR cc_start: 0.8687 (m-10) cc_final: 0.8395 (m-10) REVERT: K 235 THR cc_start: 0.8761 (p) cc_final: 0.8483 (p) REVERT: L 215 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5876 (pm20) outliers start: 193 outliers final: 120 residues processed: 430 average time/residue: 0.1880 time to fit residues: 136.2905 Evaluate side-chains 388 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 256 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 GLN Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 190 optimal weight: 0.8980 chunk 357 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 335 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.115284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073433 restraints weight = 87621.154| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.07 r_work: 0.2996 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35407 Z= 0.234 Angle : 0.669 9.461 48859 Z= 0.357 Chirality : 0.046 0.312 5582 Planarity : 0.005 0.060 5648 Dihedral : 22.097 175.781 6444 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.98 % Allowed : 25.74 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.23 (0.14), residues: 3850 helix: 0.87 (0.13), residues: 1570 sheet: -0.19 (0.29), residues: 331 loop : -0.99 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 244 TYR 0.020 0.001 TYR J 184 PHE 0.021 0.002 PHE K 179 TRP 0.013 0.001 TRP L 166 HIS 0.040 0.001 HIS D 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (35400) covalent geometry : angle 0.66916 / 0.36 (48853) hydrogen bonds : bond 0.04935 / 3.43 ( 1651) hydrogen bonds : angle 4.72009 / 3.35 ( 4452) metal coordination : bond 0.01039 / 0.52 ( 7) metal coordination : angle 0.98709 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 249 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2923 (OUTLIER) cc_final: 0.1971 (mmm) REVERT: B 75 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 79 ASN cc_start: 0.9228 (m-40) cc_final: 0.9019 (m-40) REVERT: B 179 ASP cc_start: 0.8268 (t0) cc_final: 0.7892 (t70) REVERT: C 232 GLN cc_start: 0.8125 (mp10) cc_final: 0.7601 (mp10) REVERT: C 238 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (mm) REVERT: C 467 ARG cc_start: 0.8292 (tpp80) cc_final: 0.8079 (tpp80) REVERT: C 505 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7843 (ttp-170) REVERT: C 667 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8372 (ptp-110) REVERT: C 673 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7915 (ptm160) REVERT: C 767 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8597 (pt0) REVERT: C 926 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8702 (mpp) REVERT: D 143 MET cc_start: 0.8530 (tmm) cc_final: 0.8261 (tmm) REVERT: D 259 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: D 435 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.8866 (pp30) REVERT: D 450 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8968 (tp30) REVERT: D 451 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9248 (mp) REVERT: D 845 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8200 (p) REVERT: D 1199 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.2433 (pm20) REVERT: E 41 ASP cc_start: 0.8788 (p0) cc_final: 0.8546 (p0) REVERT: F 278 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7294 (ttm110) REVERT: F 297 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8826 (mp0) REVERT: F 427 ILE cc_start: 0.8900 (tp) cc_final: 0.8642 (tp) REVERT: F 502 ARG cc_start: 0.8274 (mmp-170) cc_final: 0.7738 (mmm160) REVERT: J 159 ASP cc_start: 0.8856 (t0) cc_final: 0.8474 (t0) REVERT: J 164 GLU cc_start: 0.8725 (pm20) cc_final: 0.7872 (pm20) REVERT: J 210 ASP cc_start: 0.8529 (t0) cc_final: 0.8272 (t0) REVERT: O 217 TYR cc_start: 0.3430 (OUTLIER) cc_final: 0.2930 (t80) REVERT: K 183 ARG cc_start: 0.8363 (ptt90) cc_final: 0.7950 (ptm160) REVERT: K 213 VAL cc_start: 0.9230 (m) cc_final: 0.8802 (p) REVERT: K 217 TYR cc_start: 0.8760 (m-10) cc_final: 0.8435 (m-10) REVERT: L 215 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5980 (pm20) REVERT: I 259 ARG cc_start: -0.1946 (OUTLIER) cc_final: -0.2193 (ptt-90) REVERT: I 301 LEU cc_start: 0.3414 (OUTLIER) cc_final: 0.2505 (pp) outliers start: 194 outliers final: 136 residues processed: 420 average time/residue: 0.2009 time to fit residues: 142.1731 Evaluate side-chains 400 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 245 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 813 GLN Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1199 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 259 ARG Chi-restraints excluded: chain I residue 263 CYS Chi-restraints excluded: chain I residue 287 ARG Chi-restraints excluded: chain I residue 288 ASN Chi-restraints excluded: chain I residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 67 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 279 optimal weight: 0.6980 chunk 384 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 813 GLN E 70 GLN M 212 ASN ** K 188 ASN ** 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 = 0.3961 r_free = 0.3961 target = 0.117130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076242 restraints weight = 87742.554| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.34 r_work: 0.3032 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35407 Z= 0.136 Angle : 0.624 7.965 48859 Z= 0.334 Chirality : 0.045 0.314 5582 Planarity : 0.004 0.059 5648 Dihedral : 22.049 177.724 6444 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.02 % Allowed : 26.88 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.08 (0.14), residues: 3850 helix: 1.09 (0.13), residues: 1544 sheet: -0.20 (0.28), residues: 350 loop : -0.95 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.021 0.001 TYR J 184 PHE 0.018 0.001 PHE K 153 TRP 0.012 0.001 TRP L 166 HIS 0.025 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (35400) covalent geometry : angle 0.62352 / 0.33 (48853) hydrogen bonds : bond 0.04489 / 3.12 ( 1651) hydrogen bonds : angle 4.59829 / 3.26 ( 4452) metal coordination : bond 0.00304 / 0.14 ( 7) metal coordination : angle 1.07099 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 267 time to evaluate : 1.303 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: B 1 MET cc_start: 0.3067 (OUTLIER) cc_final: 0.2267 (mmm) REVERT: B 2 LEU cc_start: 0.8020 (mm) cc_final: 0.7810 (tp) REVERT: B 75 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 179 ASP cc_start: 0.8297 (t0) cc_final: 0.7999 (t0) REVERT: B 189 PHE cc_start: 0.8172 (m-80) cc_final: 0.7690 (m-80) REVERT: C 232 GLN cc_start: 0.8070 (mp10) cc_final: 0.7556 (mp10) REVERT: C 238 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (mm) REVERT: C 467 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7993 (tpp80) REVERT: C 505 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7917 (ttp-170) REVERT: C 569 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: C 571 VAL cc_start: 0.9137 (t) cc_final: 0.8748 (p) REVERT: C 667 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8930 (ptp-110) REVERT: C 843 GLU cc_start: 0.8536 (pm20) cc_final: 0.7817 (pm20) REVERT: C 1005 ASP cc_start: 0.8799 (p0) cc_final: 0.8481 (p0) REVERT: D 259 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: D 435 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9038 (pm20) REVERT: D 450 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8945 (tp30) REVERT: D 451 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9217 (mp) REVERT: D 497 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8597 (pp) REVERT: D 882 GLN cc_start: 0.8918 (pt0) cc_final: 0.8500 (pp30) REVERT: D 1199 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.2318 (pm20) REVERT: E 41 ASP cc_start: 0.8780 (p0) cc_final: 0.8523 (p0) REVERT: E 70 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7050 (pp30) REVERT: F 271 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5825 (pp20) REVERT: F 427 ILE cc_start: 0.8894 (tp) cc_final: 0.8615 (tp) REVERT: F 502 ARG cc_start: 0.8238 (mmp-170) cc_final: 0.7717 (mmm160) REVERT: J 159 ASP cc_start: 0.8865 (t0) cc_final: 0.8461 (t0) REVERT: J 164 GLU cc_start: 0.8697 (pm20) cc_final: 0.7865 (pm20) REVERT: J 210 ASP cc_start: 0.8552 (t0) cc_final: 0.8284 (t0) REVERT: K 167 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7593 (mtpt) REVERT: K 183 ARG cc_start: 0.8355 (ptt90) cc_final: 0.7938 (ptm160) REVERT: K 213 VAL cc_start: 0.9220 (m) cc_final: 0.8787 (p) REVERT: K 217 TYR cc_start: 0.8784 (m-10) cc_final: 0.8452 (m-10) REVERT: L 215 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: I 301 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.2831 (pp) outliers start: 163 outliers final: 111 residues processed: 407 average time/residue: 0.2019 time to fit residues: 138.1919 Evaluate side-chains 381 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 255 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1199 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 220 TYR Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 287 ARG Chi-restraints excluded: chain I residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 400 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 351 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 124 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** K 188 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.117220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076730 restraints weight = 86758.575| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.39 r_work: 0.3032 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35407 Z= 0.142 Angle : 0.616 9.221 48859 Z= 0.330 Chirality : 0.045 0.307 5582 Planarity : 0.004 0.060 5648 Dihedral : 22.013 177.036 6444 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.75 % Allowed : 26.73 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.03 (0.14), residues: 3850 helix: 1.09 (0.13), residues: 1551 sheet: -0.02 (0.29), residues: 339 loop : -0.93 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.019 0.001 TYR J 184 PHE 0.019 0.001 PHE K 153 TRP 0.012 0.001 TRP L 166 HIS 0.021 0.001 HIS D 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (35400) covalent geometry : angle 0.61557 / 0.33 (48853) hydrogen bonds : bond 0.04455 / 3.11 ( 1651) hydrogen bonds : angle 4.56180 / 3.24 ( 4452) metal coordination : bond 0.00396 / 0.18 ( 7) metal coordination : angle 0.98662 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 260 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: B 179 ASP cc_start: 0.8319 (t0) cc_final: 0.8011 (t0) REVERT: C 232 GLN cc_start: 0.8058 (mp10) cc_final: 0.7550 (mp10) REVERT: C 238 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (mm) REVERT: C 467 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7963 (tpp80) REVERT: C 569 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: C 571 VAL cc_start: 0.9123 (t) cc_final: 0.8736 (p) REVERT: C 667 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8933 (ptp-110) REVERT: C 767 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8619 (pt0) REVERT: C 843 GLU cc_start: 0.8530 (pm20) cc_final: 0.8000 (pm20) REVERT: C 1005 ASP cc_start: 0.8802 (p0) cc_final: 0.8491 (p0) REVERT: D 435 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9031 (pm20) REVERT: D 451 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9235 (mp) REVERT: D 497 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8604 (pp) REVERT: D 882 GLN cc_start: 0.8895 (pt0) cc_final: 0.8499 (pp30) REVERT: D 1199 GLU cc_start: 0.4254 (OUTLIER) cc_final: 0.2320 (pm20) REVERT: E 41 ASP cc_start: 0.8760 (p0) cc_final: 0.8522 (p0) REVERT: F 271 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5902 (pp20) REVERT: F 278 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7295 (ttm110) REVERT: F 427 ILE cc_start: 0.8899 (tp) cc_final: 0.8628 (tp) REVERT: F 502 ARG cc_start: 0.8233 (mmp-170) cc_final: 0.7633 (mmm160) REVERT: J 159 ASP cc_start: 0.8875 (t0) cc_final: 0.8472 (t0) REVERT: J 164 GLU cc_start: 0.8694 (pm20) cc_final: 0.7880 (pm20) REVERT: J 210 ASP cc_start: 0.8556 (t0) cc_final: 0.8289 (t0) REVERT: K 167 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7653 (mtpt) REVERT: K 183 ARG cc_start: 0.8360 (ptt90) cc_final: 0.7934 (ptm160) REVERT: K 213 VAL cc_start: 0.9222 (m) cc_final: 0.8790 (p) REVERT: K 217 TYR cc_start: 0.8811 (m-10) cc_final: 0.8472 (m-10) REVERT: L 193 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7358 (mm) REVERT: L 215 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: I 301 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.2692 (pp) outliers start: 154 outliers final: 113 residues processed: 395 average time/residue: 0.1964 time to fit residues: 130.8508 Evaluate side-chains 379 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 252 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1199 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 220 TYR Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 335 optimal weight: 2.9990 chunk 299 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 442 GLN C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 813 GLN E 70 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** K 188 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.114769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072859 restraints weight = 87893.631| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.07 r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 35407 Z= 0.249 Angle : 0.682 8.839 48859 Z= 0.362 Chirality : 0.047 0.293 5582 Planarity : 0.005 0.062 5648 Dihedral : 22.046 176.503 6443 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.02 % Allowed : 26.48 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.15 (0.14), residues: 3850 helix: 0.96 (0.13), residues: 1570 sheet: -0.18 (0.29), residues: 329 loop : -0.96 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 505 TYR 0.017 0.001 TYR J 184 PHE 0.020 0.002 PHE K 179 TRP 0.013 0.001 TRP L 166 HIS 0.037 0.002 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (35400) covalent geometry : angle 0.68223 / 0.36 (48853) hydrogen bonds : bond 0.04945 / 3.43 ( 1651) hydrogen bonds : angle 4.67615 / 3.32 ( 4452) metal coordination : bond 0.01109 / 0.56 ( 7) metal coordination : angle 0.98318 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 245 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.9040 (tt0) cc_final: 0.8492 (tt0) REVERT: B 75 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: B 179 ASP cc_start: 0.8321 (t0) cc_final: 0.8007 (t0) REVERT: B 189 PHE cc_start: 0.8176 (m-80) cc_final: 0.7797 (m-80) REVERT: C 232 GLN cc_start: 0.8099 (mp10) cc_final: 0.7573 (mp10) REVERT: C 238 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8382 (mm) REVERT: C 467 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7997 (tpp80) REVERT: C 569 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: C 586 MET cc_start: 0.9436 (ptm) cc_final: 0.9214 (ttp) REVERT: C 667 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8400 (ptp-110) REVERT: C 767 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8638 (pt0) REVERT: C 843 GLU cc_start: 0.8593 (pm20) cc_final: 0.7844 (pm20) REVERT: D 389 ARG cc_start: 0.8981 (ptm160) cc_final: 0.8665 (mtm110) REVERT: D 435 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.9208 (pm20) REVERT: D 451 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9262 (mp) REVERT: D 515 MET cc_start: 0.8732 (mtt) cc_final: 0.8457 (mtt) REVERT: D 845 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 1199 GLU cc_start: 0.4444 (OUTLIER) cc_final: 0.2476 (pm20) REVERT: E 41 ASP cc_start: 0.8818 (p0) cc_final: 0.8572 (p0) REVERT: E 70 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7080 (pp30) REVERT: F 278 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7293 (ttm110) REVERT: F 297 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: F 502 ARG cc_start: 0.8251 (mmp-170) cc_final: 0.7627 (mmm160) REVERT: J 159 ASP cc_start: 0.8882 (t0) cc_final: 0.8463 (t0) REVERT: J 164 GLU cc_start: 0.8709 (pm20) cc_final: 0.7904 (pm20) REVERT: J 210 ASP cc_start: 0.8576 (t0) cc_final: 0.8307 (t0) REVERT: K 167 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7678 (mtpt) REVERT: K 183 ARG cc_start: 0.8371 (ptt90) cc_final: 0.7960 (ptm160) REVERT: K 213 VAL cc_start: 0.9268 (m) cc_final: 0.8828 (p) REVERT: K 217 TYR cc_start: 0.8874 (m-10) cc_final: 0.8538 (m-10) REVERT: L 215 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5928 (pm20) REVERT: I 301 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.2522 (pp) outliers start: 163 outliers final: 120 residues processed: 391 average time/residue: 0.1877 time to fit residues: 124.3986 Evaluate side-chains 371 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 237 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 GLN Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1199 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 306 optimal weight: 50.0000 chunk 240 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 386 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 238 optimal weight: 0.9990 chunk 359 optimal weight: 0.9980 chunk 363 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 813 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** K 188 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.116294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075085 restraints weight = 88289.530| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.39 r_work: 0.2997 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35407 Z= 0.145 Angle : 0.633 8.936 48859 Z= 0.338 Chirality : 0.045 0.302 5582 Planarity : 0.004 0.061 5648 Dihedral : 22.014 178.213 6443 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.22 % Allowed : 27.34 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.05 (0.14), residues: 3850 helix: 1.07 (0.13), residues: 1554 sheet: -0.04 (0.28), residues: 346 loop : -0.94 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 815 TYR 0.020 0.001 TYR J 184 PHE 0.019 0.001 PHE K 153 TRP 0.011 0.001 TRP L 166 HIS 0.007 0.001 HIS C 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (35400) covalent geometry : angle 0.63259 / 0.34 (48853) hydrogen bonds : bond 0.04602 / 3.20 ( 1651) hydrogen bonds : angle 4.58881 / 3.26 ( 4452) metal coordination : bond 0.00463 / 0.22 ( 7) metal coordination : angle 0.99679 / 0.43 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 259 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.9041 (tt0) cc_final: 0.8495 (tt0) REVERT: B 1 MET cc_start: 0.2756 (OUTLIER) cc_final: 0.1841 (mmm) REVERT: B 179 ASP cc_start: 0.8299 (t0) cc_final: 0.7971 (t0) REVERT: B 189 PHE cc_start: 0.8188 (m-80) cc_final: 0.7820 (m-80) REVERT: C 103 MET cc_start: 0.8488 (ppp) cc_final: 0.8244 (ppp) REVERT: C 232 GLN cc_start: 0.8082 (mp10) cc_final: 0.7551 (mp10) REVERT: C 238 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 467 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7919 (tpp80) REVERT: C 569 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: C 586 MET cc_start: 0.9372 (ptm) cc_final: 0.9155 (ttp) REVERT: C 667 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8929 (ptp-110) REVERT: C 767 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8628 (pt0) REVERT: C 843 GLU cc_start: 0.8558 (pm20) cc_final: 0.7955 (pm20) REVERT: D 389 ARG cc_start: 0.9036 (ptm160) cc_final: 0.8709 (mtm110) REVERT: D 435 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9210 (pm20) REVERT: D 451 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9208 (mp) REVERT: D 515 MET cc_start: 0.8711 (mtt) cc_final: 0.8501 (mtt) REVERT: D 845 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8029 (p) REVERT: D 882 GLN cc_start: 0.8929 (pt0) cc_final: 0.8497 (pp30) REVERT: D 983 MET cc_start: 0.8910 (mmm) cc_final: 0.8551 (mmm) REVERT: D 1199 GLU cc_start: 0.4314 (OUTLIER) cc_final: 0.2385 (pm20) REVERT: E 41 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (p0) REVERT: F 278 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7335 (ttm110) REVERT: F 297 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: F 502 ARG cc_start: 0.8243 (mmp-170) cc_final: 0.7648 (mmm160) REVERT: J 159 ASP cc_start: 0.8888 (t0) cc_final: 0.8468 (t0) REVERT: J 164 GLU cc_start: 0.8685 (pm20) cc_final: 0.7894 (pm20) REVERT: J 210 ASP cc_start: 0.8623 (t0) cc_final: 0.8351 (t0) REVERT: K 167 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7788 (mtpt) REVERT: K 183 ARG cc_start: 0.8359 (ptt90) cc_final: 0.7937 (ptm160) REVERT: K 213 VAL cc_start: 0.9252 (m) cc_final: 0.8807 (p) REVERT: K 217 TYR cc_start: 0.8872 (m-10) cc_final: 0.8542 (m-10) REVERT: L 193 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7273 (mm) REVERT: L 215 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5992 (pm20) REVERT: I 301 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3062 (pp) outliers start: 137 outliers final: 114 residues processed: 380 average time/residue: 0.1891 time to fit residues: 122.0182 Evaluate side-chains 379 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 250 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 GLN Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1199 GLU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 36 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 chunk 306 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 393 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 GLN E 70 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** K 188 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.115284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073284 restraints weight = 88052.582| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.09 r_work: 0.2996 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35407 Z= 0.219 Angle : 0.653 8.320 48859 Z= 0.348 Chirality : 0.046 0.295 5582 Planarity : 0.004 0.062 5648 Dihedral : 22.011 177.776 6443 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.62 % Allowed : 27.13 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % 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: -0.09 (0.14), residues: 3850 helix: 1.02 (0.13), residues: 1566 sheet: -0.08 (0.28), residues: 338 loop : -0.95 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 259 TYR 0.021 0.001 TYR F 258 PHE 0.019 0.002 PHE K 153 TRP 0.012 0.001 TRP L 166 HIS 0.009 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (35400) covalent geometry : angle 0.65334 / 0.35 (48853) hydrogen bonds : bond 0.04715 / 3.27 ( 1651) hydrogen bonds : angle 4.61528 / 3.28 ( 4452) metal coordination : bond 0.00908 / 0.45 ( 7) metal coordination : angle 1.02477 / 0.51 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10827.25 seconds wall clock time: 185 minutes 35.50 seconds (11135.50 seconds total)