Starting phenix.real_space_refine on Mon Sep 14 11:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.map" model { file = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvy_21407/09_2026/6vvy_21407.cif" } resolution = 3.42 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= 0.010 sd= 0.100 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 130 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18419 2.51 5 N 5360 2.21 5 O 6022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30033 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} 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: 8602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8602 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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: "F" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2540 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1329 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'SRN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19151 SG CYS D 891 114.427 87.983 101.912 1.00107.18 S ATOM 19718 SG CYS D 968 110.721 89.343 99.950 1.00109.86 S ATOM 19760 SG CYS D 975 111.169 87.573 103.277 1.00 99.50 S ATOM 19778 SG CYS D 978 112.636 90.886 103.362 1.00101.12 S ATOM 12589 SG CYS D 60 58.527 65.810 68.098 1.00134.42 S ATOM 12607 SG CYS D 62 56.513 65.426 65.129 1.00140.17 S ATOM 12716 SG CYS D 75 59.982 64.685 64.300 1.00136.37 S ATOM 12742 SG CYS D 78 60.678 68.084 65.453 1.00135.88 S Time building chain proxies: 6.78, per 1000 atoms: 0.23 Number of scatterers: 30033 At special positions: 0 Unit cell: (141.9, 168.3, 190.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 130 15.00 Mg 1 11.99 O 6022 8.00 N 5360 7.00 C 18419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " 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 ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " Number of angles added : 12 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 41 sheets defined 42.0% alpha, 13.6% beta 51 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 226 removed outlier: 3.782A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.977A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.758A pdb=" N ARG B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.504A pdb=" N GLU B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 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 126 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.129A 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 removed outlier: 3.600A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 4.069A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.581A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.557A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.609A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.588A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.870A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.640A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.790A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1091 Processing helix chain 'C' and resid 1098 through 1109 Processing helix chain 'C' and resid 1118 through 1131 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.570A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.841A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 183 removed outlier: 4.300A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.745A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.216A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.811A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.671A pdb=" N GLN D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.213A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 removed outlier: 4.177A 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 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.609A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.914A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.628A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.603A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.688A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.163A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 884 No H-bonds generated for 'chain 'D' and resid 882 through 884' Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 975 through 980 removed outlier: 4.000A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.612A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1143 Proline residue: D1127 - end of helix removed outlier: 3.756A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.737A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1182 through 1195 removed outlier: 4.125A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.971A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.507A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1237 removed outlier: 4.371A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1255 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.873A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.641A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.057A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.903A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 3.592A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.627A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 438 removed outlier: 3.549A pdb=" N ASP F 437 " --> pdb=" O GLN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.585A pdb=" N ALA F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 removed outlier: 3.576A pdb=" N ILE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG F 515 " --> pdb=" O MET F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 520 Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.842A pdb=" N LEU F 527 " --> pdb=" O ARG F 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 100 through 118 removed outlier: 3.781A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.578A pdb=" N ALA M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.563A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 22 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.077A 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: 4.248A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.526A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.674A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.606A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.776A 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: 3.503A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.548A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.506A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.673A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR M 45 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.520A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'C' and resid 188 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.268A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (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 541 through 542 removed outlier: 3.584A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.710A 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: 6.792A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.516A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.128A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.751A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (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: 6.681A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.562A pdb=" N LEU D 497 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.831A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 removed outlier: 3.585A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.555A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.105A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.598A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.757A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1053 through 1056 removed outlier: 4.162A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1165 through 1167 removed outlier: 3.642A pdb=" N ARG D1204 " --> pdb=" O THR D1166 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.509A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 440 through 441 removed outlier: 5.643A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 39 through 42 1192 hydrogen bonds defined for protein. 3411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 131 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4969 1.31 - 1.43: 8044 1.43 - 1.56: 17341 1.56 - 1.69: 277 1.69 - 1.81: 178 Bond restraints: 30809 Sorted by residual: bond pdb=" C9 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.429 1.807 -0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.434 1.789 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" C28 SRN C1201 " pdb=" C29 SRN C1201 " ideal model delta sigma weight residual 1.330 1.607 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C13 SRN C1201 " pdb=" C14 SRN C1201 " ideal model delta sigma weight residual 1.328 1.601 -0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C24 SRN C1201 " pdb=" C25 SRN C1201 " ideal model delta sigma weight residual 1.328 1.570 -0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 30804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 42074 4.29 - 8.58: 194 8.58 - 12.87: 15 12.87 - 17.16: 2 17.16 - 21.45: 1 Bond angle restraints: 42286 Sorted by residual: angle pdb=" N ARG D1013 " pdb=" CA ARG D1013 " pdb=" C ARG D1013 " ideal model delta sigma weight residual 108.99 122.55 -13.56 1.57e+00 4.06e-01 7.46e+01 angle pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " pdb=" C9 SRN C1201 " ideal model delta sigma weight residual 108.56 87.11 21.45 3.00e+00 1.11e-01 5.11e+01 angle pdb=" N ILE D 916 " pdb=" CA ILE D 916 " pdb=" C ILE D 916 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N GLN D 657 " pdb=" CA GLN D 657 " pdb=" C GLN D 657 " ideal model delta sigma weight residual 109.81 121.16 -11.35 2.21e+00 2.05e-01 2.64e+01 angle pdb=" C3' DT O 42 " pdb=" O3' DT O 42 " pdb=" P DT O 43 " ideal model delta sigma weight residual 119.70 125.78 -6.08 1.20e+00 6.94e-01 2.57e+01 ... (remaining 42281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 17359 34.88 - 69.76: 1147 69.76 - 104.64: 23 104.64 - 139.52: 2 139.52 - 174.40: 8 Dihedral angle restraints: 18539 sinusoidal: 8467 harmonic: 10072 Sorted by residual: dihedral pdb=" CA ARG D 834 " pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta harmonic sigma weight residual -180.00 -122.06 -57.94 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ARG C 282 " pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta harmonic sigma weight residual 180.00 -127.80 -52.20 0 5.00e+00 4.00e-02 1.09e+02 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 180.00 143.48 36.52 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 18536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3999 0.073 - 0.146: 739 0.146 - 0.219: 64 0.219 - 0.292: 13 0.292 - 0.365: 5 Chirality restraints: 4820 Sorted by residual: chirality pdb=" C35 SRN C1201 " pdb=" C34 SRN C1201 " pdb=" C8 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C8 SRN C1201 " pdb=" C35 SRN C1201 " pdb=" C7 SRN C1201 " pdb=" O3 SRN C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ARG D1013 " pdb=" N ARG D1013 " pdb=" C ARG D1013 " pdb=" CB ARG D1013 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4817 not shown) Planarity restraints: 5100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 834 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO D 835 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 835 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 835 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 282 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO C 283 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 11 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO M 12 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO M 12 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO M 12 " -0.045 5.00e-02 4.00e+02 ... (remaining 5097 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1046 2.69 - 3.24: 26753 3.24 - 3.79: 49808 3.79 - 4.35: 58695 4.35 - 4.90: 98266 Nonbonded interactions: 234568 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.135 2.170 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D2002 " model vdw 2.174 2.170 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.209 2.170 nonbonded pdb=" O LEU D1010 " pdb=" O THR D1011 " model vdw 2.223 3.040 nonbonded pdb=" OP1 DA P 107 " pdb=" OG SER M 121 " model vdw 2.238 3.040 ... (remaining 234563 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 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.970 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 36.580 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.010 0.378 30817 Z= 0.506 Angle : 0.976 46.328 42298 Z= 0.564 Chirality : 0.056 0.365 4820 Planarity : 0.007 0.127 5100 Dihedral : 20.030 174.402 12059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.64 % Favored : 92.28 % Rotamer: Outliers : 4.85 % Allowed : 22.94 % Favored : 72.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.11), residues: 3496 helix: -2.22 (0.10), residues: 1367 sheet: -2.56 (0.23), residues: 400 loop : -2.97 (0.12), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 624 TYR 0.024 0.002 TYR A 168 PHE 0.020 0.002 PHE C 906 TRP 0.013 0.002 TRP M 85 HIS 0.009 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.50 (30809) covalent geometry : angle 0.92392 / 0.56 (42286) hydrogen bonds : bond 0.16506 / 11.64 ( 1317) hydrogen bonds : angle 7.00061 / 4.89 ( 3673) metal coordination : bond 0.15427 / 7.66 ( 8) metal coordination : angle 18.72055 / 9.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 183 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9174 (ptp) cc_final: 0.8859 (ptm) REVERT: C 154 MET cc_start: 0.9283 (tpp) cc_final: 0.9045 (tpp) REVERT: C 208 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8298 (ptm160) REVERT: C 355 MET cc_start: 0.8253 (tmm) cc_final: 0.7979 (tmm) REVERT: C 404 MET cc_start: 0.8789 (ttm) cc_final: 0.8406 (ttp) REVERT: C 584 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8524 (ptt90) REVERT: C 607 MET cc_start: 0.9077 (mtt) cc_final: 0.8825 (mtm) REVERT: C 805 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (ttmm) REVERT: C 1017 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: D 160 LYS cc_start: 0.8908 (tptp) cc_final: 0.8679 (tppt) REVERT: D 205 MET cc_start: 0.8277 (tpt) cc_final: 0.7814 (tpt) REVERT: D 1025 THR cc_start: 0.8110 (m) cc_final: 0.7802 (p) REVERT: D 1140 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8435 (tm-30) REVERT: E 31 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.8955 (p) REVERT: E 35 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8926 (mm) REVERT: F 237 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9088 (mmtm) REVERT: F 281 MET cc_start: 0.9152 (ttt) cc_final: 0.8018 (ttt) REVERT: M 52 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8511 (p0) outliers start: 142 outliers final: 33 residues processed: 320 average time/residue: 0.1949 time to fit residues: 102.0795 Evaluate side-chains 172 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1239 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 237 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 52 ASN Chi-restraints excluded: chain M residue 61 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS B 124 HIS C 141 ASN C 142 ASN C 419 ASN C 585 GLN C 662 HIS C 920 HIS D 368 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 639 GLN D 653 HIS D 657 GLN D 693 GLN D 797 ASN D1145 GLN D1227 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 388 GLN F 459 GLN F 461 GLN J 22 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.055515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037346 restraints weight = 144970.218| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.69 r_work: 0.2625 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30817 Z= 0.140 Angle : 0.642 10.711 42298 Z= 0.344 Chirality : 0.045 0.275 4820 Planarity : 0.006 0.106 5100 Dihedral : 19.789 172.061 5432 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.76 % Allowed : 23.42 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -2.35 (0.13), residues: 3496 helix: -0.34 (0.13), residues: 1374 sheet: -2.05 (0.24), residues: 391 loop : -2.51 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 144 TYR 0.013 0.001 TYR D 241 PHE 0.016 0.001 PHE D 532 TRP 0.019 0.001 TRP D 656 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (30809) covalent geometry : angle 0.63659 / 0.34 (42286) hydrogen bonds : bond 0.04861 / 3.34 ( 1317) hydrogen bonds : angle 5.17688 / 3.56 ( 3673) metal coordination : bond 0.01051 / 0.46 ( 8) metal coordination : angle 5.10934 / 2.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 135 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8860 (ptm-80) REVERT: B 71 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: C 103 MET cc_start: 0.9253 (ptp) cc_final: 0.9007 (ptm) REVERT: C 208 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8849 (ptm160) REVERT: C 355 MET cc_start: 0.8451 (tmm) cc_final: 0.7977 (tmm) REVERT: C 404 MET cc_start: 0.9202 (ttm) cc_final: 0.8749 (ttm) REVERT: C 435 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: C 514 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8447 (t) REVERT: C 672 MET cc_start: 0.9209 (mmm) cc_final: 0.8827 (mmm) REVERT: C 757 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9303 (tp) REVERT: C 805 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: C 1051 MET cc_start: 0.9055 (tpp) cc_final: 0.8757 (tpp) REVERT: C 1076 MET cc_start: 0.9491 (mmm) cc_final: 0.9281 (mmm) REVERT: D 1 MET cc_start: 0.6224 (pmm) cc_final: 0.6020 (pmm) REVERT: D 108 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9198 (tttm) REVERT: D 160 LYS cc_start: 0.9157 (tptp) cc_final: 0.8924 (tppt) REVERT: D 205 MET cc_start: 0.8446 (tpt) cc_final: 0.7919 (tpt) REVERT: D 327 MET cc_start: 0.9046 (tpp) cc_final: 0.8783 (tpp) REVERT: D 1025 THR cc_start: 0.8081 (m) cc_final: 0.7677 (p) REVERT: D 1112 MET cc_start: 0.9199 (mmm) cc_final: 0.8917 (mmm) REVERT: D 1140 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9061 (tm-30) REVERT: E 35 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9012 (mm) REVERT: F 237 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9121 (mmtp) REVERT: F 263 MET cc_start: 0.9685 (tpt) cc_final: 0.8897 (tpt) REVERT: F 281 MET cc_start: 0.9332 (ttt) cc_final: 0.8608 (ttt) REVERT: F 282 MET cc_start: 0.9276 (mmp) cc_final: 0.8979 (mmp) REVERT: F 372 MET cc_start: 0.8997 (mmm) cc_final: 0.8691 (mpp) REVERT: F 403 MET cc_start: 0.7974 (mtt) cc_final: 0.7642 (mtt) REVERT: M 85 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7039 (t60) REVERT: M 127 MET cc_start: 0.9195 (ttt) cc_final: 0.8848 (ttt) outliers start: 110 outliers final: 35 residues processed: 237 average time/residue: 0.1784 time to fit residues: 71.4561 Evaluate side-chains 172 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1136 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 237 LYS Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 85 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 79 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 334 optimal weight: 50.0000 chunk 177 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 333 optimal weight: 50.0000 chunk 179 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN D 341 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 687 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.054447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.036324 restraints weight = 146653.626| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.66 r_work: 0.2591 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30817 Z= 0.235 Angle : 0.651 9.609 42298 Z= 0.346 Chirality : 0.045 0.292 4820 Planarity : 0.005 0.114 5100 Dihedral : 19.643 172.479 5389 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.17 % Allowed : 23.25 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3496 helix: 0.40 (0.14), residues: 1382 sheet: -1.79 (0.25), residues: 401 loop : -2.28 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 584 TYR 0.013 0.001 TYR F 346 PHE 0.014 0.001 PHE C 430 TRP 0.019 0.001 TRP D 656 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (30809) covalent geometry : angle 0.64632 / 0.35 (42286) hydrogen bonds : bond 0.04944 / 3.41 ( 1317) hydrogen bonds : angle 4.91574 / 3.39 ( 3673) metal coordination : bond 0.00982 / 0.43 ( 8) metal coordination : angle 4.85070 / 2.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 130 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8869 (ptm-80) REVERT: B 71 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: C 103 MET cc_start: 0.9298 (ptp) cc_final: 0.9062 (ptm) REVERT: C 116 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: C 208 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8957 (ptt90) REVERT: C 355 MET cc_start: 0.8417 (tmm) cc_final: 0.7882 (tmm) REVERT: C 404 MET cc_start: 0.9170 (ttm) cc_final: 0.8721 (ttm) REVERT: C 672 MET cc_start: 0.9254 (mmm) cc_final: 0.8839 (mmm) REVERT: C 805 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (ttmm) REVERT: C 1051 MET cc_start: 0.9187 (tpp) cc_final: 0.8808 (tpp) REVERT: C 1063 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8128 (t80) REVERT: C 1136 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: D 108 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9218 (tttm) REVERT: D 160 LYS cc_start: 0.9163 (tptp) cc_final: 0.8955 (tppt) REVERT: D 205 MET cc_start: 0.8463 (tpt) cc_final: 0.7956 (tpt) REVERT: D 327 MET cc_start: 0.9078 (tpp) cc_final: 0.8722 (tpp) REVERT: D 1025 THR cc_start: 0.8087 (m) cc_final: 0.7703 (p) REVERT: D 1112 MET cc_start: 0.9224 (mmm) cc_final: 0.8926 (mmm) REVERT: D 1140 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9086 (tm-30) REVERT: E 35 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9045 (mm) REVERT: F 511 MET cc_start: 0.9062 (mmm) cc_final: 0.8745 (mmm) REVERT: M 127 MET cc_start: 0.9328 (ttt) cc_final: 0.9086 (ttt) outliers start: 122 outliers final: 66 residues processed: 240 average time/residue: 0.1743 time to fit residues: 71.0960 Evaluate side-chains 200 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 125 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1136 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 0.0060 chunk 320 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.037202 restraints weight = 143434.028| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.63 r_work: 0.2626 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30817 Z= 0.131 Angle : 0.584 10.920 42298 Z= 0.311 Chirality : 0.044 0.295 4820 Planarity : 0.005 0.105 5100 Dihedral : 19.512 172.524 5385 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.55 % Allowed : 23.32 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3496 helix: 0.83 (0.14), residues: 1385 sheet: -1.48 (0.26), residues: 401 loop : -2.06 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.011 0.001 TYR D 241 PHE 0.010 0.001 PHE C 430 TRP 0.022 0.001 TRP D 656 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (30809) covalent geometry : angle 0.58165 / 0.31 (42286) hydrogen bonds : bond 0.04268 / 2.94 ( 1317) hydrogen bonds : angle 4.59681 / 3.17 ( 3673) metal coordination : bond 0.00492 / 0.21 ( 8) metal coordination : angle 3.36925 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 129 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: A 18 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8693 (ptm-80) REVERT: B 71 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: C 103 MET cc_start: 0.9291 (ptp) cc_final: 0.9034 (ptm) REVERT: C 116 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8498 (mttp) REVERT: C 231 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7034 (mmt180) REVERT: C 355 MET cc_start: 0.8290 (tmm) cc_final: 0.7850 (tmm) REVERT: C 396 MET cc_start: 0.9211 (ttp) cc_final: 0.8794 (tmm) REVERT: C 404 MET cc_start: 0.9141 (ttm) cc_final: 0.8687 (ttm) REVERT: C 672 MET cc_start: 0.9257 (mmm) cc_final: 0.8866 (mmm) REVERT: C 805 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8674 (ttmm) REVERT: C 1051 MET cc_start: 0.9239 (tpp) cc_final: 0.8823 (tpp) REVERT: D 108 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9130 (tttm) REVERT: D 160 LYS cc_start: 0.9185 (tptp) cc_final: 0.8957 (tppt) REVERT: D 205 MET cc_start: 0.8420 (tpt) cc_final: 0.7935 (tpt) REVERT: D 327 MET cc_start: 0.9123 (tpp) cc_final: 0.8720 (tpp) REVERT: D 1025 THR cc_start: 0.8062 (m) cc_final: 0.7664 (p) REVERT: D 1112 MET cc_start: 0.9219 (mmm) cc_final: 0.8983 (mmm) REVERT: D 1140 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9075 (tm-30) REVERT: F 263 MET cc_start: 0.9740 (tpt) cc_final: 0.8967 (mmm) REVERT: F 281 MET cc_start: 0.9415 (ttt) cc_final: 0.8831 (ttm) outliers start: 104 outliers final: 58 residues processed: 225 average time/residue: 0.1820 time to fit residues: 68.8348 Evaluate side-chains 190 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 4 optimal weight: 0.9980 chunk 312 optimal weight: 0.0270 chunk 170 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 359 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** 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 = 0.3357 r_free = 0.3357 target = 0.054970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036848 restraints weight = 145957.579| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.68 r_work: 0.2611 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30817 Z= 0.171 Angle : 0.592 8.783 42298 Z= 0.314 Chirality : 0.043 0.291 4820 Planarity : 0.005 0.105 5100 Dihedral : 19.461 173.102 5379 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.72 % Allowed : 23.42 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -0.93 (0.14), residues: 3496 helix: 1.07 (0.14), residues: 1386 sheet: -1.40 (0.26), residues: 398 loop : -1.91 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 667 TYR 0.010 0.001 TYR D 241 PHE 0.011 0.001 PHE C 430 TRP 0.025 0.001 TRP D 656 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (30809) covalent geometry : angle 0.58970 / 0.31 (42286) hydrogen bonds : bond 0.04323 / 2.98 ( 1317) hydrogen bonds : angle 4.53028 / 3.13 ( 3673) metal coordination : bond 0.00751 / 0.34 ( 8) metal coordination : angle 3.41741 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 126 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 18 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8813 (ptm-80) REVERT: B 71 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: C 103 MET cc_start: 0.9300 (ptp) cc_final: 0.9034 (ptm) REVERT: C 116 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: C 231 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7087 (mpt180) REVERT: C 264 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9298 (tppt) REVERT: C 355 MET cc_start: 0.8213 (tmm) cc_final: 0.7893 (tmm) REVERT: C 396 MET cc_start: 0.9260 (ttp) cc_final: 0.8972 (tmm) REVERT: C 404 MET cc_start: 0.9138 (ttm) cc_final: 0.8693 (ttm) REVERT: C 435 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: C 672 MET cc_start: 0.9270 (mmm) cc_final: 0.8891 (mmm) REVERT: C 805 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (ttmm) REVERT: C 1051 MET cc_start: 0.9243 (tpp) cc_final: 0.8804 (tpp) REVERT: C 1063 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8130 (t80) REVERT: D 160 LYS cc_start: 0.9165 (tptp) cc_final: 0.8942 (tppt) REVERT: D 205 MET cc_start: 0.8381 (tpt) cc_final: 0.8047 (tpt) REVERT: D 327 MET cc_start: 0.9173 (tpp) cc_final: 0.8944 (tpt) REVERT: D 576 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: D 1025 THR cc_start: 0.8066 (m) cc_final: 0.7669 (p) REVERT: D 1112 MET cc_start: 0.9178 (mmm) cc_final: 0.8934 (mmm) REVERT: D 1140 GLU cc_start: 0.9442 (tm-30) cc_final: 0.9072 (tm-30) outliers start: 109 outliers final: 68 residues processed: 228 average time/residue: 0.1708 time to fit residues: 66.3683 Evaluate side-chains 201 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 124 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.054518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.036331 restraints weight = 146702.450| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.64 r_work: 0.2592 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30817 Z= 0.239 Angle : 0.631 8.496 42298 Z= 0.334 Chirality : 0.045 0.292 4820 Planarity : 0.005 0.108 5100 Dihedral : 19.493 173.074 5379 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.17 % Allowed : 23.42 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3496 helix: 1.15 (0.14), residues: 1385 sheet: -1.36 (0.26), residues: 405 loop : -1.90 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 667 TYR 0.014 0.001 TYR D1142 PHE 0.013 0.001 PHE C 430 TRP 0.023 0.001 TRP D 656 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (30809) covalent geometry : angle 0.62792 / 0.33 (42286) hydrogen bonds : bond 0.04648 / 3.20 ( 1317) hydrogen bonds : angle 4.60702 / 3.19 ( 3673) metal coordination : bond 0.01178 / 0.56 ( 8) metal coordination : angle 3.81356 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 126 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: A 18 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8808 (ptm-80) REVERT: B 71 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 103 MET cc_start: 0.9298 (ptp) cc_final: 0.9035 (ptm) REVERT: C 116 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8469 (mttp) REVERT: C 231 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7154 (mpt180) REVERT: C 264 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9324 (tppt) REVERT: C 355 MET cc_start: 0.8334 (tmm) cc_final: 0.7740 (tmm) REVERT: C 396 MET cc_start: 0.9312 (ttp) cc_final: 0.9029 (tmm) REVERT: C 404 MET cc_start: 0.9134 (ttm) cc_final: 0.8727 (ttm) REVERT: C 435 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: C 672 MET cc_start: 0.9264 (mmm) cc_final: 0.8896 (mmm) REVERT: C 805 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8726 (ttmm) REVERT: C 1051 MET cc_start: 0.9224 (tpp) cc_final: 0.8869 (tpp) REVERT: C 1063 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8125 (t80) REVERT: D 160 LYS cc_start: 0.9176 (tptp) cc_final: 0.8957 (tppt) REVERT: D 205 MET cc_start: 0.8410 (tpt) cc_final: 0.7962 (tpt) REVERT: D 327 MET cc_start: 0.9182 (tpp) cc_final: 0.8831 (tpp) REVERT: D 576 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8605 (mtp) REVERT: D 1025 THR cc_start: 0.8120 (m) cc_final: 0.7728 (p) REVERT: D 1112 MET cc_start: 0.9196 (mmm) cc_final: 0.8897 (mmm) REVERT: D 1140 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9084 (tm-30) REVERT: J 57 ARG cc_start: 0.9460 (OUTLIER) cc_final: 0.9168 (ptm160) outliers start: 122 outliers final: 85 residues processed: 236 average time/residue: 0.1828 time to fit residues: 73.1596 Evaluate side-chains 222 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 126 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 VAL 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 427 ILE Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 330 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 327 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036632 restraints weight = 145124.424| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.65 r_work: 0.2607 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30817 Z= 0.180 Angle : 0.599 8.462 42298 Z= 0.318 Chirality : 0.044 0.292 4820 Planarity : 0.005 0.105 5100 Dihedral : 19.452 172.813 5379 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.79 % Allowed : 24.21 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3496 helix: 1.27 (0.14), residues: 1387 sheet: -1.28 (0.26), residues: 412 loop : -1.85 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 109 TYR 0.012 0.001 TYR D1142 PHE 0.012 0.001 PHE C 430 TRP 0.018 0.001 TRP D 656 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (30809) covalent geometry : angle 0.59680 / 0.32 (42286) hydrogen bonds : bond 0.04354 / 2.99 ( 1317) hydrogen bonds : angle 4.49744 / 3.11 ( 3673) metal coordination : bond 0.00885 / 0.43 ( 8) metal coordination : angle 3.31402 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 130 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 18 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8330 (ptm-80) REVERT: A 151 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8561 (mm110) REVERT: B 71 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: C 103 MET cc_start: 0.9320 (ptp) cc_final: 0.9050 (ptm) REVERT: C 116 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8577 (mttp) REVERT: C 231 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7196 (mpt180) REVERT: C 264 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9313 (tppt) REVERT: C 355 MET cc_start: 0.8314 (tmm) cc_final: 0.7785 (tmm) REVERT: C 396 MET cc_start: 0.9327 (ttp) cc_final: 0.8935 (tmm) REVERT: C 404 MET cc_start: 0.9116 (ttm) cc_final: 0.8714 (ttm) REVERT: C 435 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: C 672 MET cc_start: 0.9244 (mmm) cc_final: 0.8893 (mmm) REVERT: C 805 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: C 926 MET cc_start: 0.8877 (mmm) cc_final: 0.8542 (mmt) REVERT: C 1017 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8910 (mp0) REVERT: C 1051 MET cc_start: 0.9251 (tpp) cc_final: 0.8869 (tpp) REVERT: D 160 LYS cc_start: 0.9193 (tptp) cc_final: 0.8976 (tppt) REVERT: D 205 MET cc_start: 0.8395 (tpt) cc_final: 0.7957 (tpt) REVERT: D 327 MET cc_start: 0.9186 (tpp) cc_final: 0.8845 (tpp) REVERT: D 576 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8586 (mtp) REVERT: D 663 MET cc_start: 0.8793 (mmm) cc_final: 0.8590 (mmm) REVERT: D 1025 THR cc_start: 0.8092 (m) cc_final: 0.7693 (p) REVERT: D 1112 MET cc_start: 0.9231 (mmm) cc_final: 0.9019 (mmm) REVERT: D 1140 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9096 (tm-30) REVERT: F 263 MET cc_start: 0.9761 (mmm) cc_final: 0.9090 (mmm) REVERT: J 57 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.9137 (ptm160) outliers start: 111 outliers final: 84 residues processed: 232 average time/residue: 0.1841 time to fit residues: 72.4644 Evaluate side-chains 220 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 125 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 50.0000 chunk 264 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 215 optimal weight: 0.0170 chunk 353 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036822 restraints weight = 145112.633| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.64 r_work: 0.2614 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30817 Z= 0.160 Angle : 0.584 8.552 42298 Z= 0.310 Chirality : 0.043 0.294 4820 Planarity : 0.004 0.103 5100 Dihedral : 19.402 172.770 5379 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.62 % Allowed : 24.21 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -0.59 (0.15), residues: 3496 helix: 1.41 (0.14), residues: 1383 sheet: -1.26 (0.26), residues: 419 loop : -1.76 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.010 0.001 TYR D1142 PHE 0.010 0.001 PHE C 430 TRP 0.019 0.001 TRP D 656 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (30809) covalent geometry : angle 0.58214 / 0.31 (42286) hydrogen bonds : bond 0.04188 / 2.87 ( 1317) hydrogen bonds : angle 4.42581 / 3.07 ( 3673) metal coordination : bond 0.00742 / 0.36 ( 8) metal coordination : angle 2.98833 / 1.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 128 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: A 18 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8300 (ptm-80) REVERT: A 151 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8578 (mm110) REVERT: B 71 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: C 103 MET cc_start: 0.9320 (ptp) cc_final: 0.9045 (ptm) REVERT: C 116 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8458 (mttm) REVERT: C 154 MET cc_start: 0.9479 (mmm) cc_final: 0.8837 (mmm) REVERT: C 231 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7207 (mpt180) REVERT: C 264 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9305 (tppt) REVERT: C 355 MET cc_start: 0.8375 (tmm) cc_final: 0.7919 (tmm) REVERT: C 396 MET cc_start: 0.9329 (ttp) cc_final: 0.9007 (tmm) REVERT: C 404 MET cc_start: 0.9140 (ttm) cc_final: 0.8715 (ttm) REVERT: C 435 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: C 672 MET cc_start: 0.9261 (mmm) cc_final: 0.8926 (mmm) REVERT: C 805 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: C 926 MET cc_start: 0.8900 (mmm) cc_final: 0.8565 (mmt) REVERT: C 1051 MET cc_start: 0.9238 (tpp) cc_final: 0.8905 (tpp) REVERT: D 108 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9089 (tttm) REVERT: D 160 LYS cc_start: 0.9200 (tptp) cc_final: 0.8976 (tppt) REVERT: D 205 MET cc_start: 0.8391 (tpt) cc_final: 0.7957 (tpt) REVERT: D 327 MET cc_start: 0.9213 (tpp) cc_final: 0.9011 (tpt) REVERT: D 576 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8601 (mtp) REVERT: D 1025 THR cc_start: 0.8102 (m) cc_final: 0.7692 (p) REVERT: D 1112 MET cc_start: 0.9241 (mmm) cc_final: 0.9038 (mmm) REVERT: D 1140 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9076 (tm-30) REVERT: F 281 MET cc_start: 0.9339 (ttm) cc_final: 0.9105 (ttm) REVERT: J 57 ARG cc_start: 0.9445 (OUTLIER) cc_final: 0.9141 (ptm160) outliers start: 106 outliers final: 83 residues processed: 224 average time/residue: 0.1802 time to fit residues: 68.4917 Evaluate side-chains 219 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 125 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 138 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 247 optimal weight: 0.0000 chunk 217 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS C 875 GLN C1054 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS J 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037670 restraints weight = 144321.824| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.66 r_work: 0.2644 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30817 Z= 0.113 Angle : 0.562 9.459 42298 Z= 0.299 Chirality : 0.043 0.298 4820 Planarity : 0.005 0.099 5100 Dihedral : 19.314 172.723 5379 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.73 % Allowed : 24.99 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -0.39 (0.15), residues: 3496 helix: 1.58 (0.14), residues: 1378 sheet: -0.97 (0.27), residues: 401 loop : -1.69 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.010 0.001 TYR D 241 PHE 0.009 0.001 PHE C 431 TRP 0.024 0.001 TRP D 656 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (30809) covalent geometry : angle 0.56077 / 0.30 (42286) hydrogen bonds : bond 0.03822 / 2.62 ( 1317) hydrogen bonds : angle 4.27482 / 2.97 ( 3673) metal coordination : bond 0.00319 / 0.16 ( 8) metal coordination : angle 2.42616 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 133 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 18 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8361 (ptm-80) REVERT: A 151 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8537 (mm110) REVERT: B 71 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: C 103 MET cc_start: 0.9307 (ptp) cc_final: 0.9030 (ptm) REVERT: C 116 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8621 (mttp) REVERT: C 154 MET cc_start: 0.9435 (mmm) cc_final: 0.8725 (mmm) REVERT: C 231 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7163 (mpt180) REVERT: C 264 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9317 (tppt) REVERT: C 355 MET cc_start: 0.8420 (tmm) cc_final: 0.8005 (tmm) REVERT: C 396 MET cc_start: 0.9285 (ttp) cc_final: 0.8917 (tmm) REVERT: C 404 MET cc_start: 0.9133 (ttm) cc_final: 0.8694 (ttm) REVERT: C 435 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 607 MET cc_start: 0.9143 (mtm) cc_final: 0.8918 (mtm) REVERT: C 630 MET cc_start: 0.9252 (tpp) cc_final: 0.9027 (tpp) REVERT: C 672 MET cc_start: 0.9239 (mmm) cc_final: 0.8900 (mmm) REVERT: C 805 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8777 (ttpt) REVERT: C 926 MET cc_start: 0.8827 (mmm) cc_final: 0.8531 (mmt) REVERT: C 1031 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8791 (mtm) REVERT: C 1051 MET cc_start: 0.9255 (tpp) cc_final: 0.8908 (tpp) REVERT: D 160 LYS cc_start: 0.9198 (tptp) cc_final: 0.8965 (tppt) REVERT: D 205 MET cc_start: 0.8378 (tpt) cc_final: 0.7942 (tpt) REVERT: D 327 MET cc_start: 0.9221 (tpp) cc_final: 0.9004 (tpt) REVERT: D 576 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8602 (mtp) REVERT: D 663 MET cc_start: 0.8754 (mmm) cc_final: 0.8548 (mmm) REVERT: D 1012 MET cc_start: 0.7462 (mpp) cc_final: 0.7244 (mpp) REVERT: D 1025 THR cc_start: 0.8088 (m) cc_final: 0.7686 (p) REVERT: D 1140 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9089 (tm-30) REVERT: J 57 ARG cc_start: 0.9437 (OUTLIER) cc_final: 0.9140 (ptm160) outliers start: 80 outliers final: 60 residues processed: 205 average time/residue: 0.1863 time to fit residues: 64.6428 Evaluate side-chains 202 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 270 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 341 optimal weight: 50.0000 chunk 267 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036618 restraints weight = 145375.059| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.66 r_work: 0.2607 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30817 Z= 0.213 Angle : 0.614 11.954 42298 Z= 0.322 Chirality : 0.044 0.302 4820 Planarity : 0.005 0.103 5100 Dihedral : 19.353 173.387 5379 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.77 % Allowed : 25.03 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -0.44 (0.15), residues: 3496 helix: 1.49 (0.14), residues: 1389 sheet: -1.12 (0.26), residues: 424 loop : -1.67 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 350 TYR 0.011 0.001 TYR D 106 PHE 0.011 0.001 PHE C 431 TRP 0.015 0.001 TRP D 656 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (30809) covalent geometry : angle 0.61201 / 0.32 (42286) hydrogen bonds : bond 0.04271 / 2.93 ( 1317) hydrogen bonds : angle 4.40339 / 3.06 ( 3673) metal coordination : bond 0.00969 / 0.47 ( 8) metal coordination : angle 3.25920 / 1.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6992 Ramachandran restraints generated. 3496 Oldfield, 0 Emsley, 3496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 132 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: A 18 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8760 (ptm-80) REVERT: A 151 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8607 (mm110) REVERT: B 71 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: C 103 MET cc_start: 0.9341 (ptp) cc_final: 0.9067 (ptm) REVERT: C 116 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8608 (mttp) REVERT: C 231 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7283 (mpt180) REVERT: C 264 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9329 (tppt) REVERT: C 355 MET cc_start: 0.8391 (tmm) cc_final: 0.7962 (tmm) REVERT: C 396 MET cc_start: 0.9311 (ttp) cc_final: 0.8978 (tmm) REVERT: C 404 MET cc_start: 0.9133 (ttm) cc_final: 0.8711 (ttm) REVERT: C 435 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: C 672 MET cc_start: 0.9253 (mmm) cc_final: 0.8904 (mmm) REVERT: C 805 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (ttmm) REVERT: C 926 MET cc_start: 0.8898 (mmm) cc_final: 0.8600 (mmt) REVERT: C 1051 MET cc_start: 0.9263 (tpp) cc_final: 0.8914 (tpp) REVERT: D 160 LYS cc_start: 0.9212 (tptp) cc_final: 0.8986 (tppt) REVERT: D 205 MET cc_start: 0.8390 (tpt) cc_final: 0.7958 (tpt) REVERT: D 310 MET cc_start: 0.9239 (tpp) cc_final: 0.8950 (mmt) REVERT: D 327 MET cc_start: 0.9228 (tpp) cc_final: 0.9025 (tpt) REVERT: D 576 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8617 (mtp) REVERT: D 663 MET cc_start: 0.8809 (mmm) cc_final: 0.8600 (mmm) REVERT: D 688 MET cc_start: 0.9271 (mmp) cc_final: 0.9041 (mmt) REVERT: D 1025 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7747 (p) REVERT: D 1140 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9075 (tm-30) REVERT: E 42 GLU cc_start: 0.8612 (tt0) cc_final: 0.8202 (tm-30) REVERT: J 57 ARG cc_start: 0.9452 (OUTLIER) cc_final: 0.9133 (ptm160) outliers start: 81 outliers final: 66 residues processed: 204 average time/residue: 0.1836 time to fit residues: 63.1914 Evaluate side-chains 204 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 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 435 GLN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 272 optimal weight: 0.0470 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037675 restraints weight = 144886.362| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.67 r_work: 0.2644 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30817 Z= 0.115 Angle : 0.572 12.417 42298 Z= 0.301 Chirality : 0.043 0.303 4820 Planarity : 0.005 0.099 5100 Dihedral : 19.285 172.755 5379 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.66 % Allowed : 25.30 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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: -0.28 (0.15), residues: 3496 helix: 1.61 (0.14), residues: 1384 sheet: -0.84 (0.27), residues: 401 loop : -1.60 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 350 TYR 0.010 0.001 TYR D 241 PHE 0.011 0.001 PHE C 252 TRP 0.023 0.001 TRP D 656 HIS 0.004 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (30809) covalent geometry : angle 0.57071 / 0.30 (42286) hydrogen bonds : bond 0.03774 / 2.58 ( 1317) hydrogen bonds : angle 4.24375 / 2.95 ( 3673) metal coordination : bond 0.00362 / 0.18 ( 8) metal coordination : angle 2.51305 / 1.42 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6991.72 seconds wall clock time: 120 minutes 41.92 seconds (7241.92 seconds total)