Starting phenix.real_space_refine on Sat Feb 7 17:26:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji5_61497/02_2026/9ji5_61497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji5_61497/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ji5_61497/02_2026/9ji5_61497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji5_61497/02_2026/9ji5_61497.map" model { file = "/net/cci-nas-00/data/ceres_data/9ji5_61497/02_2026/9ji5_61497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji5_61497/02_2026/9ji5_61497.cif" } 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-2.0-5952/lib/python3.9/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: 7.60, per 1000 atoms: 0.22 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: 3.24 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 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: 4.77 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: 9.83 Time building geometry restraints manager: 4.04 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=" N LYS K 195 " pdb=" CA LYS K 195 " ideal model delta sigma weight residual 1.462 1.491 -0.029 9.50e-03 1.11e+04 9.42e+00 bond pdb=" N VAL M 172 " pdb=" CA VAL M 172 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.32e+00 bond pdb=" CA VAL D 110 " pdb=" CB VAL D 110 " ideal model delta sigma weight residual 1.539 1.555 -0.016 5.40e-03 3.43e+04 9.02e+00 bond pdb=" N GLU D1073 " pdb=" CA GLU D1073 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.21e-02 6.83e+03 8.97e+00 bond pdb=" N LEU J 174 " pdb=" CA LEU J 174 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 35395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 46936 1.73 - 3.47: 1684 3.47 - 5.20: 188 5.20 - 6.93: 30 6.93 - 8.67: 15 Bond angle restraints: 48853 Sorted by residual: angle pdb=" CA LYS M 167 " pdb=" C LYS M 167 " pdb=" O LYS M 167 " ideal model delta sigma weight residual 122.64 118.04 4.60 1.25e+00 6.40e-01 1.35e+01 angle pdb=" CA TYR M 217 " pdb=" CB TYR M 217 " pdb=" CG TYR M 217 " ideal model delta sigma weight residual 113.90 120.47 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" N ASP D 535 " pdb=" CA ASP D 535 " pdb=" C ASP D 535 " ideal model delta sigma weight residual 110.46 105.15 5.31 1.48e+00 4.57e-01 1.29e+01 angle pdb=" CB ILE D 800 " pdb=" CG1 ILE D 800 " pdb=" CD1 ILE D 800 " ideal model delta sigma weight residual 113.80 121.14 -7.34 2.10e+00 2.27e-01 1.22e+01 angle pdb=" N PRO N 196 " pdb=" CA PRO N 196 " pdb=" C PRO N 196 " ideal model delta sigma weight residual 113.78 108.17 5.61 1.62e+00 3.81e-01 1.20e+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: 4840 0.067 - 0.133: 697 0.133 - 0.200: 38 0.200 - 0.267: 3 0.267 - 0.333: 4 Chirality restraints: 5582 Sorted by residual: 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=" 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 2.35 -2.67 -0.33 2.00e-01 2.50e+01 2.65e+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: 14.600 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: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 41.710 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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: 59.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 35407 Z= 0.226 Angle : 0.722 8.666 48859 Z= 0.417 Chirality : 0.046 0.333 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 covalent geometry : bond 0.00429 (35400) covalent geometry : angle 0.72159 (48853) hydrogen bonds : bond 0.09227 ( 1651) hydrogen bonds : angle 5.45430 ( 4452) metal coordination : bond 0.00270 ( 7) metal coordination : angle 1.52523 ( 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 : 1.324 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: 0.2308 time to fit residues: 124.4817 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 : 1.331 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 767 HIS E 70 GLN F 434 GLN M 212 ASN O 170 GLN ** K 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073574 restraints weight = 87862.977| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.09 r_work: 0.3004 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 35407 Z= 0.258 Angle : 0.703 11.672 48859 Z= 0.374 Chirality : 0.046 0.214 5582 Planarity : 0.005 0.060 5648 Dihedral : 22.075 175.969 6451 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.58 % Allowed : 25.31 % Favored : 69.11 % 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: -0.41 (0.13), residues: 3850 helix: 0.64 (0.13), residues: 1570 sheet: -0.28 (0.28), residues: 347 loop : -1.02 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 223 TYR 0.045 0.002 TYR M 217 PHE 0.016 0.002 PHE C 153 TRP 0.019 0.002 TRP L 166 HIS 0.017 0.001 HIS K 163 Details of bonding type rmsd covalent geometry : bond 0.00598 (35400) covalent geometry : angle 0.70256 (48853) hydrogen bonds : bond 0.05161 ( 1651) hydrogen bonds : angle 4.86194 ( 4452) metal coordination : bond 0.01253 ( 7) metal coordination : angle 1.70853 ( 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 451 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 270 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8798 (p0) cc_final: 0.8536 (p0) REVERT: B 5 GLN cc_start: 0.8756 (tt0) cc_final: 0.8525 (tt0) REVERT: B 69 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 75 GLU cc_start: 0.9033 (mp0) cc_final: 0.8717 (tt0) REVERT: B 179 ASP cc_start: 0.8229 (t0) cc_final: 0.7907 (t70) REVERT: B 189 PHE cc_start: 0.8131 (m-80) cc_final: 0.7755 (m-80) REVERT: C 232 GLN cc_start: 0.8028 (mp10) cc_final: 0.7462 (mp10) REVERT: C 467 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7968 (tpp80) REVERT: C 1129 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.9166 (mt0) REVERT: D 435 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.8890 (pp30) REVERT: D 450 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8843 (mm-30) REVERT: D 451 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9287 (mp) REVERT: D 944 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8960 (tt) REVERT: D 963 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6725 (mtp180) REVERT: E 70 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7296 (pp30) REVERT: F 427 ILE cc_start: 0.8828 (tp) cc_final: 0.8576 (tp) REVERT: F 502 ARG cc_start: 0.8302 (mmp-170) cc_final: 0.7706 (mmm160) REVERT: J 159 ASP cc_start: 0.8745 (t0) cc_final: 0.8543 (t0) REVERT: J 184 TYR cc_start: 0.8856 (t80) cc_final: 0.8654 (t80) REVERT: J 210 ASP cc_start: 0.8340 (t0) cc_final: 0.8109 (t0) REVERT: O 215 GLU cc_start: -0.0356 (OUTLIER) cc_final: -0.1277 (pp20) REVERT: O 217 TYR cc_start: 0.3502 (OUTLIER) cc_final: 0.3045 (t80) REVERT: K 183 ARG cc_start: 0.8336 (ptt90) cc_final: 0.7881 (ptm160) REVERT: K 217 TYR cc_start: 0.8831 (m-10) cc_final: 0.8605 (m-10) REVERT: L 215 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5964 (pm20) outliers start: 181 outliers final: 84 residues processed: 434 average time/residue: 0.2120 time to fit residues: 152.2013 Evaluate side-chains 331 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 237 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 208 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 97 LEU 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 208 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 174 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 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 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 405 THR 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 587 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1129 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 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 253 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 422 VAL 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 497 LEU Chi-restraints excluded: chain D residue 579 LEU 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 863 THR 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 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 69 ASN 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 297 GLU Chi-restraints excluded: chain F residue 410 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 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 211 VAL Chi-restraints excluded: chain M residue 214 VAL 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 215 GLU 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 L residue 215 GLU Chi-restraints excluded: chain N residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 367 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 308 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN C 775 ASN 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 163 HIS M 212 ASN N 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.114979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073335 restraints weight = 87663.369| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.04 r_work: 0.2993 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35407 Z= 0.229 Angle : 0.657 8.505 48859 Z= 0.348 Chirality : 0.044 0.256 5582 Planarity : 0.005 0.077 5648 Dihedral : 21.982 175.887 6447 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 6.32 % Allowed : 25.43 % 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: -0.29 (0.13), residues: 3850 helix: 0.75 (0.13), residues: 1574 sheet: -0.19 (0.28), residues: 335 loop : -0.97 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 77 TYR 0.020 0.001 TYR J 184 PHE 0.022 0.002 PHE K 179 TRP 0.013 0.001 TRP M 203 HIS 0.007 0.001 HIS K 163 Details of bonding type rmsd covalent geometry : bond 0.00539 (35400) covalent geometry : angle 0.65666 (48853) hydrogen bonds : bond 0.04866 ( 1651) hydrogen bonds : angle 4.75966 ( 4452) metal coordination : bond 0.01004 ( 7) metal coordination : angle 1.09200 ( 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 457 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 252 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8918 (p0) cc_final: 0.8707 (p0) REVERT: B 1 MET cc_start: 0.3337 (OUTLIER) cc_final: 0.3120 (ttt) REVERT: B 75 GLU cc_start: 0.9053 (mp0) cc_final: 0.8850 (tt0) REVERT: B 179 ASP cc_start: 0.8340 (t0) cc_final: 0.8000 (t70) REVERT: C 232 GLN cc_start: 0.8098 (mp10) cc_final: 0.7560 (mp10) REVERT: C 238 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8415 (mm) REVERT: C 467 ARG cc_start: 0.8361 (tpp80) cc_final: 0.7991 (tpp80) REVERT: C 667 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8361 (ptp-110) REVERT: C 1129 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.9113 (mt0) REVERT: D 259 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: D 383 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8743 (m-30) REVERT: D 450 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8834 (mm-30) REVERT: D 497 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8638 (pp) REVERT: D 882 GLN cc_start: 0.8945 (pt0) cc_final: 0.8470 (pp30) REVERT: D 944 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8939 (tt) REVERT: D 963 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.6999 (mtp180) REVERT: D 977 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8567 (p) REVERT: E 70 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7135 (pp30) REVERT: F 297 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (mp0) REVERT: F 403 MET cc_start: 0.8575 (mmm) cc_final: 0.8305 (mmm) REVERT: F 502 ARG cc_start: 0.8289 (mmp-170) cc_final: 0.7776 (mmm160) REVERT: J 159 ASP cc_start: 0.8833 (t0) cc_final: 0.8596 (t0) REVERT: J 184 TYR cc_start: 0.8920 (t80) cc_final: 0.8494 (t80) REVERT: J 210 ASP cc_start: 0.8449 (t0) cc_final: 0.8150 (t0) REVERT: O 173 SER cc_start: 0.2175 (OUTLIER) cc_final: 0.1859 (m) REVERT: O 217 TYR cc_start: 0.3413 (OUTLIER) cc_final: 0.2964 (t80) REVERT: K 160 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8428 (tm-30) REVERT: K 183 ARG cc_start: 0.8319 (ptt90) cc_final: 0.7881 (ptm160) REVERT: K 217 TYR cc_start: 0.8902 (m-10) cc_final: 0.8639 (m-10) REVERT: L 215 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5909 (pm20) REVERT: I 251 ILE cc_start: 0.2312 (OUTLIER) cc_final: 0.1841 (mt) outliers start: 205 outliers final: 104 residues processed: 432 average time/residue: 0.2004 time to fit residues: 144.8743 Evaluate side-chains 361 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 241 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 77 ILE 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 162 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 ASP 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 165 ASP 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 B residue 208 LEU 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 174 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 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 404 MET Chi-restraints excluded: chain C residue 405 THR 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 616 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS 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 1129 GLN Chi-restraints excluded: chain C residue 1135 VAL 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 259 GLU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER 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 785 VAL Chi-restraints excluded: chain D residue 793 TYR 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 963 ARG Chi-restraints excluded: chain D residue 977 THR 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 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 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 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 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 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 175 SER Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain N residue 165 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: 1.9990 chunk 256 optimal weight: 2.9990 chunk 360 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 365 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 380 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS C 349 HIS ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D1227 GLN E 70 GLN M 212 ASN ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073208 restraints weight = 87995.724| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.41 r_work: 0.2966 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35407 Z= 0.229 Angle : 0.654 8.309 48859 Z= 0.347 Chirality : 0.044 0.197 5582 Planarity : 0.005 0.065 5648 Dihedral : 21.915 176.376 6443 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 6.32 % Allowed : 25.37 % Favored : 68.31 % 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: -0.22 (0.14), residues: 3850 helix: 0.84 (0.13), residues: 1570 sheet: -0.09 (0.29), residues: 328 loop : -0.96 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.017 0.001 TYR J 184 PHE 0.018 0.002 PHE K 153 TRP 0.012 0.001 TRP L 166 HIS 0.006 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00539 (35400) covalent geometry : angle 0.65385 (48853) hydrogen bonds : bond 0.04751 ( 1651) hydrogen bonds : angle 4.71188 ( 4452) metal coordination : bond 0.00982 ( 7) metal coordination : angle 1.00637 ( 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 460 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 255 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8980 (p0) cc_final: 0.8649 (p0) REVERT: B 1 MET cc_start: 0.3077 (OUTLIER) cc_final: 0.1761 (mmm) REVERT: B 75 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: B 179 ASP cc_start: 0.8375 (t0) cc_final: 0.8047 (t70) REVERT: C 232 GLN cc_start: 0.8146 (mp10) cc_final: 0.7568 (mp10) REVERT: C 467 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8011 (tpp80) REVERT: C 667 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8371 (ptp-110) REVERT: C 1129 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9103 (mt0) REVERT: D 259 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: D 383 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: D 450 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8909 (mm-30) REVERT: D 451 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9262 (mp) REVERT: D 497 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8666 (pp) REVERT: D 882 GLN cc_start: 0.8943 (pt0) cc_final: 0.8449 (pp30) REVERT: D 944 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8944 (tt) REVERT: D 963 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.6976 (mtp180) REVERT: D 977 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (p) REVERT: D 1199 GLU cc_start: 0.4399 (OUTLIER) cc_final: 0.2437 (pm20) REVERT: E 70 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7388 (pp30) REVERT: F 297 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: F 361 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8986 (t0) REVERT: F 502 ARG cc_start: 0.8321 (mmp-170) cc_final: 0.7816 (mmm160) REVERT: J 159 ASP cc_start: 0.8844 (t0) cc_final: 0.8578 (t0) REVERT: J 184 TYR cc_start: 0.8976 (t80) cc_final: 0.8326 (t80) REVERT: J 210 ASP cc_start: 0.8520 (t0) cc_final: 0.8214 (t0) REVERT: K 157 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7087 (mm-30) REVERT: K 167 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7727 (mtpt) REVERT: K 183 ARG cc_start: 0.8323 (ptt90) cc_final: 0.7890 (ptm160) REVERT: K 217 TYR cc_start: 0.8923 (m-10) cc_final: 0.8673 (m-10) REVERT: K 235 THR cc_start: 0.8901 (p) cc_final: 0.8693 (p) REVERT: L 215 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5879 (pm20) REVERT: I 251 ILE cc_start: 0.2405 (OUTLIER) cc_final: 0.2175 (mt) outliers start: 205 outliers final: 132 residues processed: 436 average time/residue: 0.2023 time to fit residues: 148.7916 Evaluate side-chains 386 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 237 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 77 ILE 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 57 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 75 GLU 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 208 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 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 324 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 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 589 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 654 SER 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 737 LEU 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 1129 GLN 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 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 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 383 ASP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 SER 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 583 THR 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 767 HIS Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 793 TYR 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 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 977 THR 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 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 69 ASN 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 297 GLU Chi-restraints excluded: chain F residue 361 ASP 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 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 175 SER 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 165 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 66 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 332 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 345 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN E 70 GLN N 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.115866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075119 restraints weight = 87781.627| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.38 r_work: 0.3008 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35407 Z= 0.153 Angle : 0.602 8.307 48859 Z= 0.320 Chirality : 0.042 0.216 5582 Planarity : 0.004 0.060 5648 Dihedral : 21.803 177.400 6442 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: -0.03 (0.14), residues: 3850 helix: 1.06 (0.13), residues: 1554 sheet: 0.11 (0.29), residues: 320 loop : -0.92 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.017 0.001 TYR J 184 PHE 0.019 0.001 PHE N 179 TRP 0.012 0.001 TRP L 166 HIS 0.029 0.001 HIS D 767 Details of bonding type rmsd covalent geometry : bond 0.00354 (35400) covalent geometry : angle 0.60193 (48853) hydrogen bonds : bond 0.04280 ( 1651) hydrogen bonds : angle 4.56692 ( 4452) metal coordination : bond 0.00432 ( 7) metal coordination : angle 0.77843 ( 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 445 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 270 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.9039 (tt0) cc_final: 0.8496 (tt0) REVERT: B 1 MET cc_start: 0.3233 (OUTLIER) cc_final: 0.1874 (mmm) REVERT: B 4 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 5 GLN cc_start: 0.8714 (tt0) cc_final: 0.8427 (tt0) REVERT: B 179 ASP cc_start: 0.8370 (t0) cc_final: 0.8008 (t70) REVERT: C 189 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8886 (tm-30) REVERT: C 232 GLN cc_start: 0.8123 (mp10) cc_final: 0.7554 (mp10) REVERT: C 238 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8444 (mm) REVERT: C 429 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: C 467 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7998 (tpp80) REVERT: C 569 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 667 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8873 (ptp-110) REVERT: C 843 GLU cc_start: 0.8580 (pm20) cc_final: 0.7867 (pm20) REVERT: C 1129 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.9094 (mt0) REVERT: D 259 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8870 (pm20) REVERT: D 451 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9195 (mp) REVERT: D 497 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (pp) REVERT: D 882 GLN cc_start: 0.8884 (pt0) cc_final: 0.8473 (pp30) REVERT: D 944 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8987 (tt) REVERT: D 1199 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.2359 (pm20) REVERT: D 1250 GLU cc_start: 0.8811 (pm20) cc_final: 0.8273 (pm20) REVERT: F 502 ARG cc_start: 0.8290 (mmp-170) cc_final: 0.7413 (mmm160) REVERT: J 159 ASP cc_start: 0.8839 (t0) cc_final: 0.8597 (t0) REVERT: J 164 GLU cc_start: 0.8483 (pm20) cc_final: 0.7954 (pm20) REVERT: J 184 TYR cc_start: 0.8933 (t80) cc_final: 0.8395 (t80) REVERT: J 210 ASP cc_start: 0.8552 (t0) cc_final: 0.8237 (t0) REVERT: K 157 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6881 (mm-30) REVERT: K 167 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7898 (mtpt) REVERT: K 183 ARG cc_start: 0.8323 (ptt90) cc_final: 0.7874 (ptm160) REVERT: K 213 VAL cc_start: 0.9272 (m) cc_final: 0.8739 (p) REVERT: K 217 TYR cc_start: 0.8937 (m-10) cc_final: 0.8577 (m-10) REVERT: L 215 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: I 251 ILE cc_start: 0.2367 (OUTLIER) cc_final: 0.1961 (mt) outliers start: 175 outliers final: 103 residues processed: 422 average time/residue: 0.2034 time to fit residues: 143.5675 Evaluate side-chains 365 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 247 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 77 ILE 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 162 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 60 LEU 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 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 189 GLU 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 316 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 429 GLU Chi-restraints excluded: chain C residue 442 GLN 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 616 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 926 MET 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 1129 GLN 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 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 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 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 944 LEU 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 1199 GLU 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 F residue 297 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 416 TYR 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 225 ILE 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 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 O residue 177 THR Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 211 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 242 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 190 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 284 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 96 optimal weight: 0.0040 chunk 56 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 552 GLN ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 434 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.117865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076493 restraints weight = 87237.391| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.12 r_work: 0.3071 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2987 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= 0.125 Angle : 0.581 8.793 48859 Z= 0.309 Chirality : 0.041 0.219 5582 Planarity : 0.004 0.058 5648 Dihedral : 21.664 176.877 6442 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.91 % Allowed : 27.56 % 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: 0.13 (0.14), residues: 3850 helix: 1.22 (0.14), residues: 1547 sheet: 0.07 (0.29), residues: 330 loop : -0.82 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.017 0.001 TYR J 184 PHE 0.019 0.001 PHE K 153 TRP 0.010 0.001 TRP C 938 HIS 0.006 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00276 (35400) covalent geometry : angle 0.58084 (48853) hydrogen bonds : bond 0.03876 ( 1651) hydrogen bonds : angle 4.41101 ( 4452) metal coordination : bond 0.00254 ( 7) metal coordination : angle 1.66770 ( 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 399 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 272 time to evaluate : 1.301 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: 0.8971 (tt0) cc_final: 0.8449 (tt0) REVERT: B 2 LEU cc_start: 0.7999 (mm) cc_final: 0.7793 (tp) REVERT: B 4 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 179 ASP cc_start: 0.8348 (t0) cc_final: 0.7967 (t70) REVERT: B 189 PHE cc_start: 0.8234 (m-80) cc_final: 0.7915 (m-80) REVERT: C 189 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8870 (tm-30) REVERT: C 232 GLN cc_start: 0.8026 (mp10) cc_final: 0.7475 (mp10) REVERT: C 238 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (mm) REVERT: C 467 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7970 (tpp80) REVERT: C 569 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: C 607 MET cc_start: 0.8724 (mtt) cc_final: 0.8499 (mtp) REVERT: C 843 GLU cc_start: 0.8523 (pm20) cc_final: 0.7861 (pm20) REVERT: C 1129 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9063 (mt0) REVERT: D 339 ASP cc_start: 0.9155 (t70) cc_final: 0.8887 (t0) REVERT: D 451 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9201 (mp) REVERT: D 497 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8297 (pp) REVERT: D 714 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8782 (m-30) REVERT: D 882 GLN cc_start: 0.8717 (pt0) cc_final: 0.8443 (pp30) REVERT: D 944 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8974 (tt) REVERT: D 1199 GLU cc_start: 0.4141 (OUTLIER) cc_final: 0.2244 (pm20) REVERT: D 1250 GLU cc_start: 0.8822 (pm20) cc_final: 0.8211 (pm20) REVERT: E 41 ASP cc_start: 0.8730 (p0) cc_final: 0.8529 (p0) REVERT: F 361 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8664 (t0) REVERT: F 427 ILE cc_start: 0.8923 (tp) cc_final: 0.8627 (tp) REVERT: J 159 ASP cc_start: 0.8824 (t0) cc_final: 0.8527 (t0) REVERT: J 164 GLU cc_start: 0.8487 (pm20) cc_final: 0.7989 (pm20) REVERT: J 184 TYR cc_start: 0.8921 (t80) cc_final: 0.8311 (t80) REVERT: J 210 ASP cc_start: 0.8503 (t0) cc_final: 0.8103 (t0) REVERT: J 212 ASN cc_start: 0.8770 (m110) cc_final: 0.8309 (m110) REVERT: J 215 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: K 183 ARG cc_start: 0.8371 (ptt90) cc_final: 0.7943 (ptm160) REVERT: K 213 VAL cc_start: 0.9217 (m) cc_final: 0.8745 (p) REVERT: K 217 TYR cc_start: 0.8937 (m-10) cc_final: 0.8568 (m-10) REVERT: L 215 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: I 251 ILE cc_start: 0.2145 (OUTLIER) cc_final: 0.1653 (mt) outliers start: 127 outliers final: 80 residues processed: 382 average time/residue: 0.2081 time to fit residues: 132.5414 Evaluate side-chains 346 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 252 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 65 THR 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 B residue 4 SER Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 60 LEU 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 174 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 189 GLU 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 373 PHE 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 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1129 GLN 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 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 428 SER 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 714 ASP Chi-restraints excluded: chain D residue 730 THR 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 944 LEU 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 1176 LEU Chi-restraints excluded: chain D residue 1199 GLU 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 70 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 361 ASP 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 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 217 TYR Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 211 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 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 287 ARG 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: 9.9990 chunk 279 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074998 restraints weight = 88097.830| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.46 r_work: 0.3008 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35407 Z= 0.164 Angle : 0.596 8.213 48859 Z= 0.316 Chirality : 0.042 0.220 5582 Planarity : 0.004 0.059 5648 Dihedral : 21.646 176.617 6442 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.96 % Allowed : 26.42 % Favored : 68.62 % 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: 1.22 (0.13), residues: 1553 sheet: 0.15 (0.29), residues: 328 loop : -0.80 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 502 TYR 0.015 0.001 TYR J 184 PHE 0.019 0.001 PHE K 179 TRP 0.010 0.001 TRP L 166 HIS 0.007 0.001 HIS K 163 Details of bonding type rmsd covalent geometry : bond 0.00383 (35400) covalent geometry : angle 0.59554 (48853) hydrogen bonds : bond 0.04135 ( 1651) hydrogen bonds : angle 4.42171 ( 4452) metal coordination : bond 0.00572 ( 7) metal coordination : angle 0.94649 ( 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 420 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 259 time to evaluate : 1.376 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 4 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 167 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9273 (mm) REVERT: B 179 ASP cc_start: 0.8368 (t0) cc_final: 0.7988 (t70) REVERT: C 103 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8310 (ppp) REVERT: C 189 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8866 (tm-30) REVERT: C 232 GLN cc_start: 0.8112 (mp10) cc_final: 0.7553 (mp10) REVERT: C 238 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8438 (mm) REVERT: C 250 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: C 429 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: C 467 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8144 (tpp80) REVERT: C 569 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 667 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8910 (ptp-110) REVERT: C 843 GLU cc_start: 0.8582 (pm20) cc_final: 0.7868 (pm20) REVERT: C 1129 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9116 (mt0) REVERT: D 339 ASP cc_start: 0.9183 (t70) cc_final: 0.8923 (t0) REVERT: D 450 GLU cc_start: 0.9230 (tp30) cc_final: 0.8926 (tp30) REVERT: D 451 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9213 (mp) REVERT: D 497 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8606 (pp) REVERT: D 882 GLN cc_start: 0.8807 (pt0) cc_final: 0.8460 (pp30) REVERT: D 944 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8998 (tt) REVERT: D 1199 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.2343 (pm20) REVERT: D 1250 GLU cc_start: 0.8845 (pm20) cc_final: 0.8194 (pm20) REVERT: F 361 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.9031 (t0) REVERT: J 159 ASP cc_start: 0.8824 (t0) cc_final: 0.8535 (t0) REVERT: J 164 GLU cc_start: 0.8499 (pm20) cc_final: 0.7982 (pm20) REVERT: J 184 TYR cc_start: 0.8975 (t80) cc_final: 0.8378 (t80) REVERT: J 210 ASP cc_start: 0.8534 (t0) cc_final: 0.8265 (t0) REVERT: J 215 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8432 (mm-30) REVERT: K 183 ARG cc_start: 0.8387 (ptt90) cc_final: 0.7968 (ptm160) REVERT: K 213 VAL cc_start: 0.9215 (m) cc_final: 0.8706 (p) REVERT: K 217 TYR cc_start: 0.8939 (m-10) cc_final: 0.8566 (m-10) REVERT: L 215 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5855 (pm20) REVERT: I 251 ILE cc_start: 0.2342 (OUTLIER) cc_final: 0.1883 (mt) outliers start: 161 outliers final: 113 residues processed: 401 average time/residue: 0.1955 time to fit residues: 132.8590 Evaluate side-chains 384 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 253 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 89 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 60 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 166 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 GLU 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 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 409 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 429 GLU 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 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 861 LEU 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 1129 GLN 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 210 ASP 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 428 SER 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 509 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL 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 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1033 GLU 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 1111 LEU 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 1275 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 69 ASN 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 297 GLU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 416 TYR 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 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 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 198 ILE 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 211 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 251 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 400 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.113487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072393 restraints weight = 87080.127| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.02 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35407 Z= 0.228 Angle : 0.656 15.127 48859 Z= 0.347 Chirality : 0.044 0.226 5582 Planarity : 0.005 0.059 5648 Dihedral : 21.746 178.250 6442 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.39 % Allowed : 25.83 % Favored : 68.77 % 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: 0.04 (0.14), residues: 3850 helix: 1.08 (0.13), residues: 1559 sheet: 0.04 (0.29), residues: 330 loop : -0.84 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 502 TYR 0.019 0.001 TYR F 258 PHE 0.030 0.002 PHE K 179 TRP 0.013 0.001 TRP D 723 HIS 0.009 0.001 HIS K 163 Details of bonding type rmsd covalent geometry : bond 0.00534 (35400) covalent geometry : angle 0.65586 (48853) hydrogen bonds : bond 0.04720 ( 1651) hydrogen bonds : angle 4.59225 ( 4452) metal coordination : bond 0.01038 ( 7) metal coordination : angle 1.17602 ( 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 427 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 252 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9309 (mm) REVERT: B 179 ASP cc_start: 0.8386 (t0) cc_final: 0.8015 (t0) REVERT: B 189 PHE cc_start: 0.8235 (m-80) cc_final: 0.7755 (m-80) REVERT: C 189 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: C 232 GLN cc_start: 0.8138 (mp10) cc_final: 0.7576 (mp10) REVERT: C 250 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: C 429 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: C 467 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8152 (tpp80) REVERT: C 569 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 667 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (ptp-110) REVERT: C 1129 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.9117 (mt0) REVERT: D 339 ASP cc_start: 0.9149 (t70) cc_final: 0.8877 (t0) REVERT: D 435 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.9120 (pm20) REVERT: D 450 GLU cc_start: 0.9180 (tp30) cc_final: 0.8868 (tp30) REVERT: D 451 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9253 (mp) REVERT: D 497 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 882 GLN cc_start: 0.8955 (pt0) cc_final: 0.8484 (pp30) REVERT: D 944 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9053 (tt) REVERT: D 1199 GLU cc_start: 0.4393 (OUTLIER) cc_final: 0.2486 (pm20) REVERT: D 1250 GLU cc_start: 0.8806 (pm20) cc_final: 0.8242 (pm20) REVERT: F 278 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7602 (ttm110) REVERT: F 361 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.9037 (t0) REVERT: J 159 ASP cc_start: 0.8815 (t0) cc_final: 0.8524 (t0) REVERT: J 164 GLU cc_start: 0.8539 (pm20) cc_final: 0.7953 (pm20) REVERT: J 184 TYR cc_start: 0.8929 (t80) cc_final: 0.8523 (t80) REVERT: J 210 ASP cc_start: 0.8612 (t0) cc_final: 0.8361 (t0) REVERT: J 215 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8483 (mm-30) REVERT: K 183 ARG cc_start: 0.8353 (ptt90) cc_final: 0.7946 (ptm160) REVERT: K 213 VAL cc_start: 0.9253 (m) cc_final: 0.8700 (p) REVERT: K 217 TYR cc_start: 0.8966 (m-10) cc_final: 0.8614 (m-10) REVERT: L 215 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: I 251 ILE cc_start: 0.2022 (OUTLIER) cc_final: 0.1458 (mt) outliers start: 175 outliers final: 119 residues processed: 410 average time/residue: 0.2075 time to fit residues: 142.4475 Evaluate side-chains 380 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 244 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 65 THR 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 57 ASP Chi-restraints excluded: chain B residue 60 LEU 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 167 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 ILE 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 189 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 250 GLU 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 355 MET 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 429 GLU 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 654 SER Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 861 LEU 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 1129 GLN 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 173 ARG Chi-restraints excluded: chain D residue 210 ASP 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 298 VAL 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 461 VAL 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 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 1033 GLU 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 1111 LEU 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 68 TYR 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 304 VAL Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 416 TYR 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 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 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 198 ILE Chi-restraints excluded: chain O residue 211 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 202 VAL 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 174 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 251 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 81 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 335 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073692 restraints weight = 87048.733| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.03 r_work: 0.3004 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35407 Z= 0.172 Angle : 0.613 11.494 48859 Z= 0.326 Chirality : 0.042 0.198 5582 Planarity : 0.004 0.059 5648 Dihedral : 21.690 179.659 6442 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.41 % Allowed : 26.54 % Favored : 69.05 % 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: 0.11 (0.14), residues: 3850 helix: 1.17 (0.13), residues: 1551 sheet: 0.10 (0.29), residues: 326 loop : -0.81 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.012 0.001 TYR J 184 PHE 0.021 0.001 PHE K 179 TRP 0.011 0.001 TRP L 166 HIS 0.010 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00402 (35400) covalent geometry : angle 0.61279 (48853) hydrogen bonds : bond 0.04283 ( 1651) hydrogen bonds : angle 4.49471 ( 4452) metal coordination : bond 0.00598 ( 7) metal coordination : angle 1.14060 ( 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 402 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 259 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9299 (mm) REVERT: B 179 ASP cc_start: 0.8382 (t0) cc_final: 0.7977 (t0) REVERT: C 189 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8841 (tm-30) REVERT: C 211 TRP cc_start: 0.7632 (m-10) cc_final: 0.7219 (m-90) REVERT: C 232 GLN cc_start: 0.8110 (mp10) cc_final: 0.7553 (mp10) REVERT: C 250 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 429 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: C 467 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8099 (tpp80) REVERT: C 569 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 613 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8683 (ptm-80) REVERT: C 667 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8989 (ptp-110) REVERT: C 843 GLU cc_start: 0.8631 (pm20) cc_final: 0.7806 (pm20) REVERT: C 1129 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9105 (mt0) REVERT: D 339 ASP cc_start: 0.9151 (t70) cc_final: 0.8868 (t0) REVERT: D 450 GLU cc_start: 0.9174 (tp30) cc_final: 0.8864 (tp30) REVERT: D 451 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9244 (mp) REVERT: D 497 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8622 (pp) REVERT: D 767 HIS cc_start: 0.8020 (m-70) cc_final: 0.7449 (t70) REVERT: D 882 GLN cc_start: 0.8937 (pt0) cc_final: 0.8512 (pp30) REVERT: D 1104 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.6110 (t-90) REVERT: D 1199 GLU cc_start: 0.4305 (OUTLIER) cc_final: 0.2456 (pm20) REVERT: D 1250 GLU cc_start: 0.8778 (pm20) cc_final: 0.8154 (pm20) REVERT: J 159 ASP cc_start: 0.8851 (t0) cc_final: 0.8544 (t0) REVERT: J 164 GLU cc_start: 0.8517 (pm20) cc_final: 0.7944 (pm20) REVERT: J 184 TYR cc_start: 0.8913 (t80) cc_final: 0.8532 (t80) REVERT: J 210 ASP cc_start: 0.8594 (t0) cc_final: 0.8375 (t0) REVERT: J 215 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: M 241 TYR cc_start: 0.5198 (m-80) cc_final: 0.4973 (m-80) REVERT: K 183 ARG cc_start: 0.8379 (ptt90) cc_final: 0.7966 (ptm160) REVERT: K 213 VAL cc_start: 0.9250 (m) cc_final: 0.8640 (p) REVERT: K 217 TYR cc_start: 0.8963 (m-10) cc_final: 0.8575 (m-10) REVERT: L 215 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5915 (pm20) REVERT: I 251 ILE cc_start: 0.2072 (OUTLIER) cc_final: 0.1473 (mt) REVERT: I 263 CYS cc_start: 0.5283 (OUTLIER) cc_final: 0.5037 (p) outliers start: 143 outliers final: 109 residues processed: 387 average time/residue: 0.2072 time to fit residues: 134.7423 Evaluate side-chains 374 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 249 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 60 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 167 ILE 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 B residue 234 ILE 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 189 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU 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 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 429 GLU 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 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS 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 1129 GLN 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 428 SER 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 509 ILE 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 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 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 1193 VAL Chi-restraints excluded: chain D residue 1199 GLU 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 70 GLN 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 416 TYR 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 J residue 239 VAL Chi-restraints excluded: chain M residue 152 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 198 ILE Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 202 VAL 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 174 LEU Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 263 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 306 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 386 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073422 restraints weight = 87073.627| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.04 r_work: 0.2994 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35407 Z= 0.184 Angle : 0.626 11.678 48859 Z= 0.332 Chirality : 0.043 0.205 5582 Planarity : 0.004 0.060 5648 Dihedral : 21.684 179.017 6442 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.22 % Allowed : 26.88 % Favored : 68.90 % 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: 0.11 (0.14), residues: 3850 helix: 1.15 (0.13), residues: 1552 sheet: 0.13 (0.29), residues: 334 loop : -0.80 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 502 TYR 0.022 0.001 TYR F 258 PHE 0.020 0.001 PHE K 179 TRP 0.011 0.001 TRP L 166 HIS 0.009 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00430 (35400) covalent geometry : angle 0.62562 (48853) hydrogen bonds : bond 0.04350 ( 1651) hydrogen bonds : angle 4.51416 ( 4452) metal coordination : bond 0.00695 ( 7) metal coordination : angle 0.96205 ( 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 392 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 255 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9304 (mm) REVERT: B 179 ASP cc_start: 0.8377 (t0) cc_final: 0.7977 (t0) REVERT: C 103 MET cc_start: 0.8518 (ppp) cc_final: 0.8210 (ppp) REVERT: C 189 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8852 (tm-30) REVERT: C 211 TRP cc_start: 0.7618 (m-10) cc_final: 0.7208 (m-90) REVERT: C 232 GLN cc_start: 0.8137 (mp10) cc_final: 0.7586 (mp10) REVERT: C 250 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: C 429 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: C 467 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8109 (tpp80) REVERT: C 569 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: C 613 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.8716 (ptm-80) REVERT: C 667 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8822 (ptp-110) REVERT: C 843 GLU cc_start: 0.8662 (pm20) cc_final: 0.7841 (pm20) REVERT: C 1129 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9113 (mt0) REVERT: D 339 ASP cc_start: 0.9151 (t70) cc_final: 0.8870 (t0) REVERT: D 450 GLU cc_start: 0.9170 (tp30) cc_final: 0.8870 (tp30) REVERT: D 451 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9228 (mp) REVERT: D 767 HIS cc_start: 0.8017 (m170) cc_final: 0.7471 (t70) REVERT: D 882 GLN cc_start: 0.8906 (pt0) cc_final: 0.8512 (pp30) REVERT: D 1104 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6058 (t-90) REVERT: D 1199 GLU cc_start: 0.4342 (OUTLIER) cc_final: 0.2452 (pm20) REVERT: D 1250 GLU cc_start: 0.8791 (pm20) cc_final: 0.8174 (pm20) REVERT: F 278 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7625 (ttm110) REVERT: F 297 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8856 (mp0) REVERT: J 159 ASP cc_start: 0.8855 (t0) cc_final: 0.8539 (t0) REVERT: J 164 GLU cc_start: 0.8517 (pm20) cc_final: 0.7938 (pm20) REVERT: J 184 TYR cc_start: 0.8956 (t80) cc_final: 0.8570 (t80) REVERT: J 210 ASP cc_start: 0.8580 (t0) cc_final: 0.8361 (t0) REVERT: J 215 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (tp30) REVERT: M 241 TYR cc_start: 0.5257 (m-80) cc_final: 0.5007 (m-80) REVERT: K 183 ARG cc_start: 0.8375 (ptt90) cc_final: 0.7964 (ptm160) REVERT: K 217 TYR cc_start: 0.8975 (m-10) cc_final: 0.8713 (m-10) REVERT: L 215 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5947 (pm20) REVERT: I 251 ILE cc_start: 0.1999 (OUTLIER) cc_final: 0.1396 (mt) REVERT: I 263 CYS cc_start: 0.5234 (OUTLIER) cc_final: 0.4990 (p) outliers start: 137 outliers final: 111 residues processed: 376 average time/residue: 0.2046 time to fit residues: 129.9957 Evaluate side-chains 375 residues out of total 3313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 247 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 60 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 167 ILE 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 B residue 234 ILE 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 189 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU 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 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 429 GLU 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 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1129 GLN 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 210 ASP 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 428 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL 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 733 MET Chi-restraints excluded: chain D residue 738 VAL 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 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1199 GLU 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 278 ARG Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 416 TYR 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 J residue 239 VAL Chi-restraints excluded: chain M residue 152 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 232 LEU Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 202 VAL 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 174 LEU Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 263 CYS 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: 0.9990 chunk 306 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 393 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS D 854 HIS D1227 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.116460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075756 restraints weight = 87026.647| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.06 r_work: 0.3049 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35407 Z= 0.129 Angle : 0.592 11.748 48859 Z= 0.314 Chirality : 0.042 0.194 5582 Planarity : 0.004 0.060 5648 Dihedral : 21.566 177.964 6442 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.08 % Allowed : 28.14 % Favored : 68.77 % 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: 0.22 (0.14), residues: 3850 helix: 1.27 (0.14), residues: 1547 sheet: 0.17 (0.29), residues: 347 loop : -0.76 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 502 TYR 0.015 0.001 TYR J 184 PHE 0.019 0.001 PHE K 153 TRP 0.013 0.001 TRP C 211 HIS 0.009 0.001 HIS C 841 Details of bonding type rmsd covalent geometry : bond 0.00291 (35400) covalent geometry : angle 0.59194 (48853) hydrogen bonds : bond 0.03856 ( 1651) hydrogen bonds : angle 4.39045 ( 4452) metal coordination : bond 0.00247 ( 7) metal coordination : angle 1.37886 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10935.58 seconds wall clock time: 187 minutes 13.10 seconds (11233.10 seconds total)