Starting phenix.real_space_refine on Mon Sep 14 02:42:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047.map" model { file = "/net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m7j_9047/09_2026/6m7j_9047_neut_trim.cif" } resolution = 4.4 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= 0.006 sd= 0.082 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 55 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 16871 2.51 5 N 4836 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 27183 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 2, 'C0L': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 110.355 57.512 85.944 1.00199.50 S ATOM 19692 SG CYS D 968 106.381 58.194 87.216 1.00203.67 S ATOM 19734 SG CYS D 975 107.880 59.453 84.373 1.00192.01 S ATOM 19752 SG CYS D 978 108.130 56.056 83.748 1.00186.92 S ATOM 12567 SG CYS D 60 75.458 104.029 122.731 1.00238.85 S ATOM 12585 SG CYS D 62 73.867 104.451 125.750 1.00228.37 S Time building chain proxies: 5.57, per 1000 atoms: 0.20 Number of scatterers: 27183 At special positions: 0 Unit cell: (132.6, 159.9, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 55 15.00 Mg 1 11.99 O 5320 8.00 N 4836 7.00 C 16871 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " Number of angles added : 6 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 45 sheets defined 43.2% alpha, 11.5% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.938A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 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 224 removed outlier: 3.630A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.978A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.992A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.141A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 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 241 removed outlier: 3.614A 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: 3.508A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.819A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.572A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.699A pdb=" N GLU C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.758A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.662A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.385A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 745 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.654A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 943 removed outlier: 4.292A pdb=" N ILE C 931 " --> pdb=" O ASN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1071 through 1080 removed outlier: 3.657A pdb=" N GLN C1077 " --> pdb=" O CYS C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1092 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.007A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.823A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.650A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 185 Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.401A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.534A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.136A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.794A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.570A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.646A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 3.557A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 4.339A pdb=" N ILE D 509 " --> pdb=" O ARG D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 533 removed outlier: 4.257A pdb=" N ALA D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 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 677 removed outlier: 3.830A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 728 removed outlier: 3.692A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.933A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 806 removed outlier: 4.762A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.705A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.550A pdb=" N TYR D 921 " --> pdb=" O GLU D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.758A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.537A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix Processing helix chain 'D' and resid 1151 through 1162 Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.815A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.594A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1255 removed outlier: 4.283A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 72 removed outlier: 4.079A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.736A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.386A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.761A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 447 through 466 Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.525A 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 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'F' and resid 522 through 527 removed outlier: 3.750A pdb=" N ASP F 525 " --> pdb=" O VAL F 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.819A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.607A pdb=" N THR A 175 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.537A pdb=" N ILE A 54 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.299A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.464A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 removed outlier: 3.862A pdb=" N PHE C 166 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.322A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 456 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 187 through 189 Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC2, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.596A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 561 through 562 removed outlier: 4.123A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.458A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 668 removed outlier: 4.771A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC8, first strand: chain 'C' and resid 717 through 722 removed outlier: 3.843A pdb=" N ILE C 915 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 722 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 916 " --> pdb=" O ILE C 736 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 717 " --> pdb=" O ILE C1030 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AD1, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.688A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.325A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 905 through 906 Processing sheet with id=AD5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.656A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD7, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD8, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.674A pdb=" N CYS D 75 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 80 " --> pdb=" O CYS D 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 93 through 102 removed outlier: 9.801A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 234 through 236 removed outlier: 5.812A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 611 through 612 removed outlier: 7.251A pdb=" N TYR D 612 " --> pdb=" O ARG D 636 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE4, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AE5, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 5.372A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE7, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE8, first strand: chain 'F' and resid 439 through 441 Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 45 1141 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4621 1.30 - 1.43: 6811 1.43 - 1.56: 16034 1.56 - 1.68: 115 1.68 - 1.81: 173 Bond restraints: 27754 Sorted by residual: bond pdb=" C23 C0L D1404 " pdb=" O24 C0L D1404 " ideal model delta sigma weight residual 1.204 1.389 -0.185 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C18 C0L D1404 " pdb=" O19 C0L D1404 " ideal model delta sigma weight residual 1.224 1.392 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C PHE C1068 " pdb=" N GLY C1069 " ideal model delta sigma weight residual 1.331 1.450 -0.119 1.46e-02 4.69e+03 6.66e+01 bond pdb=" CA PHE C1068 " pdb=" C PHE C1068 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.34e-02 5.57e+03 5.04e+01 bond pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 1.530 1.642 -0.111 1.69e-02 3.50e+03 4.34e+01 ... (remaining 27749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 37571 4.40 - 8.80: 228 8.80 - 13.20: 25 13.20 - 17.60: 8 17.60 - 22.00: 2 Bond angle restraints: 37834 Sorted by residual: angle pdb=" C ALA F 447 " pdb=" N VAL F 448 " pdb=" CA VAL F 448 " ideal model delta sigma weight residual 120.47 103.02 17.45 1.58e+00 4.01e-01 1.22e+02 angle pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " pdb=" CG TRP C1074 " ideal model delta sigma weight residual 113.60 133.87 -20.27 1.90e+00 2.77e-01 1.14e+02 angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.83 108.80 11.03 1.08e+00 8.57e-01 1.04e+02 angle pdb=" N TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta sigma weight residual 110.49 127.45 -16.96 1.69e+00 3.50e-01 1.01e+02 angle pdb=" N CYS C1073 " pdb=" CA CYS C1073 " pdb=" C CYS C1073 " ideal model delta sigma weight residual 110.80 94.65 16.15 2.13e+00 2.20e-01 5.75e+01 ... (remaining 37829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 16522 35.54 - 71.07: 331 71.07 - 106.61: 24 106.61 - 142.14: 1 142.14 - 177.68: 5 Dihedral angle restraints: 16883 sinusoidal: 7293 harmonic: 9590 Sorted by residual: dihedral pdb=" N TRP C1074 " pdb=" C TRP C1074 " pdb=" CA TRP C1074 " pdb=" CB TRP C1074 " ideal model delta harmonic sigma weight residual 122.80 137.25 -14.45 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" CA ARG D 480 " pdb=" C ARG D 480 " pdb=" N PRO D 481 " pdb=" CA PRO D 481 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG D 578 " pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 16880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4115 0.100 - 0.200: 182 0.200 - 0.299: 4 0.299 - 0.399: 1 0.399 - 0.499: 3 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA ALA F 225 " pdb=" N ALA F 225 " pdb=" C ALA F 225 " pdb=" CB ALA F 225 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA VAL F 446 " pdb=" N VAL F 446 " pdb=" C VAL F 446 " pdb=" CB VAL F 446 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 4302 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 223 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA F 223 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA F 223 " -0.023 2.00e-02 2.50e+03 pdb=" N SER F 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C1056 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C1056 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO C1056 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C1057 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1074 " 0.024 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP C1074 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP C1074 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1074 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1074 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1074 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1074 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C1074 " -0.000 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 128 2.21 - 2.89: 11392 2.89 - 3.56: 47263 3.56 - 4.23: 69140 4.23 - 4.90: 107087 Nonbonded interactions: 235010 Sorted by model distance: nonbonded pdb=" O ARG C 230 " pdb=" CG ARG C 231 " model vdw 1.543 3.440 nonbonded pdb=" CE MET C1051 " pdb=" CA ASP F 441 " model vdw 1.553 3.890 nonbonded pdb=" O CYS C1073 " pdb=" N ALA C1075 " model vdw 1.622 3.120 nonbonded pdb=" CE MET C1051 " pdb=" CB ASP F 441 " model vdw 1.827 3.860 nonbonded pdb=" CA GLN F 415 " pdb=" CD ARG F 418 " model vdw 1.972 3.870 ... (remaining 235005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 31.360 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 0.698 27761 Z= 0.635 Angle : 1.112 30.393 37840 Z= 0.636 Chirality : 0.050 0.499 4305 Planarity : 0.005 0.072 4789 Dihedral : 13.779 177.678 10715 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 73.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.31 % Favored : 87.45 % Rotamer: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.12), residues: 3331 helix: -2.26 (0.12), residues: 1231 sheet: -3.63 (0.22), residues: 329 loop : -3.04 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 334 TYR 0.033 0.003 TYR D 134 PHE 0.021 0.003 PHE D 7 TRP 0.061 0.004 TRP C1074 HIS 0.018 0.004 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.47 (27754) covalent geometry : angle 1.08392 / 0.63 (37834) hydrogen bonds : bond 0.22064 / 14.55 ( 1192) hydrogen bonds : angle 8.08061 / 5.59 ( 3335) metal coordination : bond 0.21209 / 10.81 ( 6) metal coordination : angle 19.68195 / 9.13 ( 6) Misc. bond : bond 0.69793 / 36.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.9239 (tp30) cc_final: 0.8983 (tm-30) REVERT: B 194 LEU cc_start: 0.9488 (mt) cc_final: 0.9078 (mp) REVERT: C 159 MET cc_start: 0.8831 (mmm) cc_final: 0.8479 (mmm) REVERT: C 611 MET cc_start: 0.9454 (mtm) cc_final: 0.8788 (mtp) REVERT: C 630 MET cc_start: 0.9284 (mmm) cc_final: 0.8869 (mmm) REVERT: C 661 MET cc_start: 0.8758 (tpt) cc_final: 0.8510 (tpt) REVERT: C 713 MET cc_start: 0.8873 (mmm) cc_final: 0.8461 (mmm) REVERT: C 724 MET cc_start: 0.9285 (ptm) cc_final: 0.8913 (ptm) REVERT: C 741 LEU cc_start: 0.9555 (mt) cc_final: 0.9342 (tt) REVERT: C 783 ASP cc_start: 0.9339 (m-30) cc_final: 0.9063 (t0) REVERT: C 904 MET cc_start: 0.9385 (tpp) cc_final: 0.8382 (mmm) REVERT: C 1028 MET cc_start: 0.9322 (ttt) cc_final: 0.8945 (tpp) REVERT: C 1031 MET cc_start: 0.7752 (mtm) cc_final: 0.7533 (mpp) REVERT: C 1127 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9263 (mt-10) REVERT: D 120 LEU cc_start: 0.9059 (mp) cc_final: 0.8805 (tp) REVERT: D 373 MET cc_start: 0.9161 (mtp) cc_final: 0.8731 (mtp) REVERT: D 379 ASP cc_start: 0.9382 (m-30) cc_final: 0.9089 (m-30) REVERT: D 657 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: D 733 MET cc_start: 0.9103 (pp-130) cc_final: 0.8878 (ppp) REVERT: D 983 MET cc_start: 0.8937 (mmm) cc_final: 0.8581 (mmt) REVERT: E 99 ILE cc_start: 0.9365 (mt) cc_final: 0.9118 (mt) REVERT: F 282 MET cc_start: 0.9765 (mmt) cc_final: 0.9554 (mmt) REVERT: F 343 PHE cc_start: 0.9252 (t80) cc_final: 0.8996 (t80) REVERT: J 69 LEU cc_start: 0.8849 (mt) cc_final: 0.8468 (tp) outliers start: 6 outliers final: 2 residues processed: 220 average time/residue: 0.1945 time to fit residues: 67.8365 Evaluate side-chains 130 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN B 61 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 GLN C 920 HIS ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN D 352 ASN D 465 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 687 GLN D 748 HIS ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN D1133 HIS D1145 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS F 322 GLN F 325 ASN F 377 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.027567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.019864 restraints weight = 308163.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.020567 restraints weight = 194403.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.021090 restraints weight = 139807.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.021460 restraints weight = 109457.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.021755 restraints weight = 91364.122| |-----------------------------------------------------------------------------| r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 27761 Z= 0.290 Angle : 0.861 14.359 37840 Z= 0.446 Chirality : 0.049 0.342 4305 Planarity : 0.007 0.097 4789 Dihedral : 16.534 170.025 4348 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 0.32 % Allowed : 2.83 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.13), residues: 3331 helix: -1.12 (0.13), residues: 1289 sheet: -3.09 (0.24), residues: 344 loop : -2.68 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 877 TYR 0.028 0.002 TYR E 56 PHE 0.024 0.002 PHE D 673 TRP 0.025 0.003 TRP C 70 HIS 0.016 0.003 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.29 (27754) covalent geometry : angle 0.85431 / 0.45 (37834) hydrogen bonds : bond 0.06549 / 4.41 ( 1192) hydrogen bonds : angle 6.55094 / 4.50 ( 3335) metal coordination : bond 0.02493 / 1.46 ( 6) metal coordination : angle 8.41309 / 4.13 ( 6) Misc. bond : bond 0.02240 / 1.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8297 (tpp) cc_final: 0.7614 (mtp) REVERT: B 192 LEU cc_start: 0.9778 (tp) cc_final: 0.9403 (pp) REVERT: C 159 MET cc_start: 0.9047 (mmm) cc_final: 0.8563 (mmm) REVERT: C 440 MET cc_start: 0.8912 (tmm) cc_final: 0.8014 (tmm) REVERT: C 586 MET cc_start: 0.8690 (pmm) cc_final: 0.8133 (pmm) REVERT: C 593 MET cc_start: 0.9077 (mmm) cc_final: 0.8838 (mmm) REVERT: C 607 MET cc_start: 0.9632 (mmp) cc_final: 0.9130 (mmm) REVERT: C 611 MET cc_start: 0.9715 (mtm) cc_final: 0.9060 (mtp) REVERT: C 630 MET cc_start: 0.9513 (mmm) cc_final: 0.9299 (mmm) REVERT: C 661 MET cc_start: 0.9003 (tpt) cc_final: 0.8614 (tpt) REVERT: C 713 MET cc_start: 0.8738 (mmm) cc_final: 0.8389 (mmm) REVERT: C 724 MET cc_start: 0.9559 (ptm) cc_final: 0.9092 (ttp) REVERT: C 741 LEU cc_start: 0.9727 (mt) cc_final: 0.9449 (tt) REVERT: C 783 ASP cc_start: 0.9408 (m-30) cc_final: 0.9140 (t0) REVERT: C 916 ILE cc_start: 0.9679 (mt) cc_final: 0.9435 (tt) REVERT: C 1031 MET cc_start: 0.8655 (mtm) cc_final: 0.7922 (mpp) REVERT: C 1076 MET cc_start: 0.9196 (ttt) cc_final: 0.8572 (tpp) REVERT: C 1127 GLU cc_start: 0.9646 (mt-10) cc_final: 0.9390 (mt-10) REVERT: D 114 LEU cc_start: 0.9691 (mt) cc_final: 0.9487 (mt) REVERT: D 373 MET cc_start: 0.9042 (mtp) cc_final: 0.8727 (mtp) REVERT: D 379 ASP cc_start: 0.9391 (m-30) cc_final: 0.9067 (m-30) REVERT: D 422 VAL cc_start: 0.8968 (m) cc_final: 0.8761 (p) REVERT: D 457 MET cc_start: 0.9699 (mtp) cc_final: 0.9475 (mtt) REVERT: D 559 MET cc_start: 0.9544 (mpp) cc_final: 0.8828 (mpp) REVERT: D 983 MET cc_start: 0.8913 (mmm) cc_final: 0.8690 (mmt) REVERT: D 1161 MET cc_start: 0.9158 (tpp) cc_final: 0.8833 (tpp) REVERT: D 1208 MET cc_start: 0.9145 (pmm) cc_final: 0.8425 (pmm) REVERT: F 281 MET cc_start: 0.9534 (ptp) cc_final: 0.9245 (ptm) REVERT: F 282 MET cc_start: 0.9779 (mmt) cc_final: 0.9507 (mmt) REVERT: F 343 PHE cc_start: 0.9195 (t80) cc_final: 0.8887 (t80) REVERT: F 511 MET cc_start: 0.9657 (tpt) cc_final: 0.9389 (tpt) REVERT: J 69 LEU cc_start: 0.8914 (mt) cc_final: 0.8706 (pp) outliers start: 9 outliers final: 1 residues processed: 163 average time/residue: 0.1749 time to fit residues: 47.4627 Evaluate side-chains 120 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 34 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 HIS C 875 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.019882 restraints weight = 302006.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.020613 restraints weight = 189299.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.021145 restraints weight = 135368.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.021530 restraints weight = 105412.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.021829 restraints weight = 87521.428| |-----------------------------------------------------------------------------| r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27761 Z= 0.203 Angle : 0.731 13.737 37840 Z= 0.379 Chirality : 0.046 0.318 4305 Planarity : 0.005 0.083 4789 Dihedral : 16.308 172.671 4348 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3331 helix: -0.32 (0.14), residues: 1285 sheet: -2.63 (0.25), residues: 347 loop : -2.36 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG D 173 TYR 0.031 0.002 TYR E 56 PHE 0.025 0.002 PHE D 131 TRP 0.019 0.002 TRP C 70 HIS 0.013 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (27754) covalent geometry : angle 0.72660 / 0.38 (37834) hydrogen bonds : bond 0.05408 / 3.66 ( 1192) hydrogen bonds : angle 6.02987 / 4.11 ( 3335) metal coordination : bond 0.00757 / 0.66 ( 6) metal coordination : angle 6.42160 / 3.07 ( 6) Misc. bond : bond 0.01663 / 0.88 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8284 (tpp) cc_final: 0.7690 (mtm) REVERT: B 96 TYR cc_start: 0.8682 (m-80) cc_final: 0.8217 (m-80) REVERT: C 159 MET cc_start: 0.8989 (mmm) cc_final: 0.8501 (mmm) REVERT: C 355 MET cc_start: 0.8536 (tmm) cc_final: 0.8125 (tmm) REVERT: C 440 MET cc_start: 0.8870 (tmm) cc_final: 0.8004 (tmm) REVERT: C 586 MET cc_start: 0.8807 (pmm) cc_final: 0.8399 (pmm) REVERT: C 593 MET cc_start: 0.9083 (mmm) cc_final: 0.8880 (mmm) REVERT: C 607 MET cc_start: 0.9635 (mmp) cc_final: 0.9164 (mmm) REVERT: C 611 MET cc_start: 0.9708 (mtm) cc_final: 0.9040 (mtp) REVERT: C 661 MET cc_start: 0.8921 (tpt) cc_final: 0.8539 (tpt) REVERT: C 713 MET cc_start: 0.8614 (mmm) cc_final: 0.8209 (mmm) REVERT: C 724 MET cc_start: 0.9524 (ptm) cc_final: 0.9249 (ttp) REVERT: C 741 LEU cc_start: 0.9702 (mt) cc_final: 0.9454 (tt) REVERT: C 783 ASP cc_start: 0.9404 (m-30) cc_final: 0.9142 (t0) REVERT: C 916 ILE cc_start: 0.9628 (mt) cc_final: 0.9324 (tp) REVERT: C 1031 MET cc_start: 0.8443 (mtm) cc_final: 0.7774 (mpp) REVERT: C 1076 MET cc_start: 0.9070 (ttt) cc_final: 0.8710 (ttt) REVERT: C 1087 GLU cc_start: 0.9092 (mp0) cc_final: 0.8824 (pt0) REVERT: C 1127 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9436 (mt-10) REVERT: D 114 LEU cc_start: 0.9722 (mt) cc_final: 0.9505 (mt) REVERT: D 143 MET cc_start: 0.8961 (ttm) cc_final: 0.8612 (ttm) REVERT: D 155 MET cc_start: 0.9333 (tpt) cc_final: 0.9021 (tpp) REVERT: D 205 MET cc_start: 0.6107 (ttm) cc_final: 0.5242 (ttm) REVERT: D 373 MET cc_start: 0.9272 (mtp) cc_final: 0.8812 (mtp) REVERT: D 379 ASP cc_start: 0.9340 (m-30) cc_final: 0.9001 (m-30) REVERT: D 422 VAL cc_start: 0.9254 (m) cc_final: 0.9013 (p) REVERT: D 457 MET cc_start: 0.9697 (mtp) cc_final: 0.9448 (mtt) REVERT: D 559 MET cc_start: 0.9547 (mpp) cc_final: 0.8848 (mpp) REVERT: D 706 MET cc_start: 0.9387 (mmp) cc_final: 0.9003 (ttt) REVERT: D 983 MET cc_start: 0.8929 (mmm) cc_final: 0.8589 (mmt) REVERT: D 1161 MET cc_start: 0.9164 (tpp) cc_final: 0.8785 (tpp) REVERT: D 1208 MET cc_start: 0.9193 (pmm) cc_final: 0.8419 (pmm) REVERT: F 281 MET cc_start: 0.9480 (ptp) cc_final: 0.9168 (ptm) REVERT: F 282 MET cc_start: 0.9767 (mmt) cc_final: 0.9460 (mmt) REVERT: F 315 MET cc_start: 0.8466 (mtt) cc_final: 0.8260 (mtt) REVERT: F 343 PHE cc_start: 0.9175 (t80) cc_final: 0.8882 (t80) REVERT: F 403 MET cc_start: 0.9088 (mmp) cc_final: 0.8867 (mmm) REVERT: F 511 MET cc_start: 0.9549 (tpt) cc_final: 0.9287 (tpp) REVERT: J 68 ASP cc_start: 0.8302 (m-30) cc_final: 0.7588 (t0) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.1785 time to fit residues: 44.9309 Evaluate side-chains 119 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 64 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 63 optimal weight: 0.0040 chunk 186 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS C 142 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.020004 restraints weight = 289374.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.020753 restraints weight = 180436.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.021304 restraints weight = 128394.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.021692 restraints weight = 99610.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.022013 restraints weight = 82882.005| |-----------------------------------------------------------------------------| r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27761 Z= 0.156 Angle : 0.682 11.708 37840 Z= 0.354 Chirality : 0.045 0.303 4305 Planarity : 0.005 0.067 4789 Dihedral : 16.091 177.040 4348 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.14), residues: 3331 helix: 0.16 (0.14), residues: 1284 sheet: -2.31 (0.26), residues: 347 loop : -2.12 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 384 TYR 0.032 0.002 TYR E 56 PHE 0.019 0.002 PHE D 452 TRP 0.016 0.002 TRP C 70 HIS 0.010 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (27754) covalent geometry : angle 0.67955 / 0.35 (37834) hydrogen bonds : bond 0.04856 / 3.29 ( 1192) hydrogen bonds : angle 5.65355 / 3.86 ( 3335) metal coordination : bond 0.00888 / 0.61 ( 6) metal coordination : angle 5.03873 / 2.22 ( 6) Misc. bond : bond 0.00666 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8244 (tpp) cc_final: 0.7591 (mtm) REVERT: B 96 TYR cc_start: 0.8720 (m-80) cc_final: 0.8219 (m-80) REVERT: C 159 MET cc_start: 0.8982 (mmm) cc_final: 0.8622 (mmm) REVERT: C 355 MET cc_start: 0.8707 (tmm) cc_final: 0.8405 (tmm) REVERT: C 440 MET cc_start: 0.8919 (tmm) cc_final: 0.8694 (tmm) REVERT: C 607 MET cc_start: 0.9681 (mmp) cc_final: 0.9213 (mmm) REVERT: C 611 MET cc_start: 0.9718 (mtm) cc_final: 0.9058 (mtp) REVERT: C 661 MET cc_start: 0.9047 (tpt) cc_final: 0.8731 (tpt) REVERT: C 713 MET cc_start: 0.8615 (mmm) cc_final: 0.8195 (mmm) REVERT: C 724 MET cc_start: 0.9561 (ptm) cc_final: 0.9166 (tmm) REVERT: C 741 LEU cc_start: 0.9702 (mt) cc_final: 0.9471 (tt) REVERT: C 783 ASP cc_start: 0.9397 (m-30) cc_final: 0.9108 (p0) REVERT: C 904 MET cc_start: 0.9295 (tpp) cc_final: 0.8920 (tpp) REVERT: C 916 ILE cc_start: 0.9627 (mt) cc_final: 0.9192 (tp) REVERT: C 1031 MET cc_start: 0.8521 (mtm) cc_final: 0.7777 (mpp) REVERT: C 1068 PHE cc_start: 0.8855 (t80) cc_final: 0.8513 (t80) REVERT: C 1076 MET cc_start: 0.9107 (ttt) cc_final: 0.8709 (ttt) REVERT: C 1127 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9454 (mt-10) REVERT: D 114 LEU cc_start: 0.9733 (mt) cc_final: 0.9322 (mt) REVERT: D 120 LEU cc_start: 0.9139 (mp) cc_final: 0.8858 (tp) REVERT: D 143 MET cc_start: 0.8925 (ttm) cc_final: 0.8498 (ttm) REVERT: D 373 MET cc_start: 0.9426 (mtp) cc_final: 0.8989 (mtp) REVERT: D 379 ASP cc_start: 0.9360 (m-30) cc_final: 0.9106 (m-30) REVERT: D 422 VAL cc_start: 0.9331 (m) cc_final: 0.9113 (p) REVERT: D 457 MET cc_start: 0.9689 (mtp) cc_final: 0.9428 (mtt) REVERT: D 1161 MET cc_start: 0.9190 (tpp) cc_final: 0.8824 (tpp) REVERT: D 1208 MET cc_start: 0.9255 (pmm) cc_final: 0.8152 (pmm) REVERT: E 55 ILE cc_start: 0.9861 (mt) cc_final: 0.9624 (tt) REVERT: E 78 TYR cc_start: 0.9178 (m-10) cc_final: 0.8975 (m-10) REVERT: F 231 TYR cc_start: 0.9049 (t80) cc_final: 0.8763 (t80) REVERT: F 263 MET cc_start: 0.9712 (tmm) cc_final: 0.9511 (tmm) REVERT: F 281 MET cc_start: 0.9485 (ptp) cc_final: 0.9195 (ptm) REVERT: F 282 MET cc_start: 0.9746 (mmt) cc_final: 0.9464 (mmt) REVERT: F 343 PHE cc_start: 0.9181 (t80) cc_final: 0.8905 (t80) REVERT: F 403 MET cc_start: 0.9022 (mmp) cc_final: 0.8776 (mmm) REVERT: F 511 MET cc_start: 0.9477 (tpt) cc_final: 0.9273 (tpp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1719 time to fit residues: 42.4116 Evaluate side-chains 119 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 254 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.027197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.019385 restraints weight = 301474.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.020095 restraints weight = 189294.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.020619 restraints weight = 135825.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.020981 restraints weight = 105911.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.021280 restraints weight = 88291.389| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 27761 Z= 0.258 Angle : 0.742 13.457 37840 Z= 0.384 Chirality : 0.045 0.299 4305 Planarity : 0.005 0.062 4789 Dihedral : 16.046 179.950 4348 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3331 helix: 0.21 (0.14), residues: 1292 sheet: -2.24 (0.27), residues: 333 loop : -2.01 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 209 TYR 0.026 0.002 TYR D 106 PHE 0.017 0.002 PHE D 452 TRP 0.015 0.002 TRP F 283 HIS 0.011 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.26 (27754) covalent geometry : angle 0.73747 / 0.38 (37834) hydrogen bonds : bond 0.05065 / 3.42 ( 1192) hydrogen bonds : angle 5.70136 / 3.89 ( 3335) metal coordination : bond 0.01536 / 1.49 ( 6) metal coordination : angle 6.57516 / 3.24 ( 6) Misc. bond : bond 0.00516 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8294 (tpp) cc_final: 0.7642 (mtp) REVERT: B 96 TYR cc_start: 0.8722 (m-80) cc_final: 0.8215 (m-80) REVERT: C 103 MET cc_start: 0.8785 (mmm) cc_final: 0.8345 (mmm) REVERT: C 355 MET cc_start: 0.8754 (tmm) cc_final: 0.8492 (tmm) REVERT: C 440 MET cc_start: 0.8844 (tmm) cc_final: 0.8330 (tmm) REVERT: C 579 MET cc_start: 0.9206 (tpt) cc_final: 0.9003 (tpt) REVERT: C 593 MET cc_start: 0.9232 (mmp) cc_final: 0.8975 (mmm) REVERT: C 607 MET cc_start: 0.9660 (mmp) cc_final: 0.9202 (mmm) REVERT: C 611 MET cc_start: 0.9701 (mtm) cc_final: 0.9022 (mtp) REVERT: C 661 MET cc_start: 0.8920 (tpt) cc_final: 0.8601 (tpt) REVERT: C 713 MET cc_start: 0.8601 (mmm) cc_final: 0.8268 (mmm) REVERT: C 724 MET cc_start: 0.9538 (ptm) cc_final: 0.9142 (ppp) REVERT: C 741 LEU cc_start: 0.9692 (mt) cc_final: 0.9458 (tt) REVERT: C 783 ASP cc_start: 0.9426 (m-30) cc_final: 0.9162 (t0) REVERT: C 904 MET cc_start: 0.9347 (tpp) cc_final: 0.8992 (tpp) REVERT: C 916 ILE cc_start: 0.9656 (mt) cc_final: 0.9256 (tp) REVERT: C 1031 MET cc_start: 0.8630 (mtm) cc_final: 0.7917 (mpp) REVERT: C 1068 PHE cc_start: 0.9014 (t80) cc_final: 0.8687 (t80) REVERT: C 1076 MET cc_start: 0.9067 (ttt) cc_final: 0.8837 (ttt) REVERT: C 1127 GLU cc_start: 0.9699 (mt-10) cc_final: 0.9469 (mt-10) REVERT: D 106 TYR cc_start: 0.9346 (m-10) cc_final: 0.8772 (m-10) REVERT: D 114 LEU cc_start: 0.9778 (mt) cc_final: 0.9498 (mt) REVERT: D 120 LEU cc_start: 0.9148 (mp) cc_final: 0.8890 (tp) REVERT: D 143 MET cc_start: 0.9009 (ttm) cc_final: 0.8624 (ttm) REVERT: D 373 MET cc_start: 0.9395 (mtp) cc_final: 0.9002 (mtp) REVERT: D 379 ASP cc_start: 0.9359 (m-30) cc_final: 0.9113 (m-30) REVERT: D 559 MET cc_start: 0.9421 (mpp) cc_final: 0.8790 (mpp) REVERT: D 1161 MET cc_start: 0.9237 (tpp) cc_final: 0.8730 (tpt) REVERT: D 1208 MET cc_start: 0.9286 (pmm) cc_final: 0.8099 (pmm) REVERT: E 55 ILE cc_start: 0.9869 (mt) cc_final: 0.9651 (tt) REVERT: F 263 MET cc_start: 0.9709 (tmm) cc_final: 0.9489 (tmm) REVERT: F 281 MET cc_start: 0.9470 (ptp) cc_final: 0.9199 (ptm) REVERT: F 282 MET cc_start: 0.9738 (mmt) cc_final: 0.9459 (mmt) REVERT: F 403 MET cc_start: 0.9021 (mmp) cc_final: 0.8792 (mmm) REVERT: F 511 MET cc_start: 0.9453 (tpt) cc_final: 0.9098 (tpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1762 time to fit residues: 39.5266 Evaluate side-chains 113 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 132 optimal weight: 0.0570 chunk 234 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 0.1980 chunk 158 optimal weight: 0.9990 overall best weight: 2.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS C 142 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.027876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.019824 restraints weight = 288194.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020572 restraints weight = 179978.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.021119 restraints weight = 128499.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.021529 restraints weight = 99664.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.021823 restraints weight = 82193.999| |-----------------------------------------------------------------------------| r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27761 Z= 0.142 Angle : 0.655 11.215 37840 Z= 0.335 Chirality : 0.045 0.306 4305 Planarity : 0.005 0.060 4789 Dihedral : 15.850 177.381 4348 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3331 helix: 0.64 (0.14), residues: 1274 sheet: -1.97 (0.27), residues: 344 loop : -1.82 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 334 TYR 0.031 0.002 TYR E 56 PHE 0.014 0.001 PHE D 452 TRP 0.016 0.001 TRP J 82 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (27754) covalent geometry : angle 0.65155 / 0.34 (37834) hydrogen bonds : bond 0.04369 / 2.93 ( 1192) hydrogen bonds : angle 5.31204 / 3.62 ( 3335) metal coordination : bond 0.00791 / 0.72 ( 6) metal coordination : angle 5.26496 / 2.58 ( 6) Misc. bond : bond 0.00447 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8190 (tpp) cc_final: 0.7684 (mtt) REVERT: B 96 TYR cc_start: 0.8763 (m-80) cc_final: 0.8250 (m-80) REVERT: C 103 MET cc_start: 0.8890 (mmm) cc_final: 0.8499 (mmm) REVERT: C 159 MET cc_start: 0.8954 (mmm) cc_final: 0.8542 (mmm) REVERT: C 440 MET cc_start: 0.8947 (tmm) cc_final: 0.8714 (tmm) REVERT: C 586 MET cc_start: 0.8671 (pmm) cc_final: 0.8279 (pmm) REVERT: C 607 MET cc_start: 0.9680 (mmp) cc_final: 0.9215 (mmm) REVERT: C 611 MET cc_start: 0.9715 (mtm) cc_final: 0.9083 (mtp) REVERT: C 661 MET cc_start: 0.9049 (tpt) cc_final: 0.8772 (tpt) REVERT: C 713 MET cc_start: 0.8586 (mmm) cc_final: 0.8247 (mmm) REVERT: C 724 MET cc_start: 0.9552 (ptm) cc_final: 0.9130 (tmm) REVERT: C 741 LEU cc_start: 0.9688 (mt) cc_final: 0.9467 (tt) REVERT: C 783 ASP cc_start: 0.9362 (m-30) cc_final: 0.9079 (p0) REVERT: C 916 ILE cc_start: 0.9669 (mt) cc_final: 0.9224 (tp) REVERT: C 1028 MET cc_start: 0.9067 (tmm) cc_final: 0.8838 (tmm) REVERT: C 1068 PHE cc_start: 0.9038 (t80) cc_final: 0.8657 (t80) REVERT: C 1076 MET cc_start: 0.9017 (ttt) cc_final: 0.8767 (ttt) REVERT: C 1127 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9441 (mt-10) REVERT: D 114 LEU cc_start: 0.9763 (mt) cc_final: 0.9465 (mt) REVERT: D 120 LEU cc_start: 0.9156 (mp) cc_final: 0.8887 (tp) REVERT: D 143 MET cc_start: 0.8967 (ttm) cc_final: 0.8566 (ttm) REVERT: D 373 MET cc_start: 0.9432 (mtp) cc_final: 0.9044 (mtp) REVERT: D 379 ASP cc_start: 0.9364 (m-30) cc_final: 0.9119 (m-30) REVERT: D 447 MET cc_start: 0.9269 (ttt) cc_final: 0.9021 (ttt) REVERT: D 559 MET cc_start: 0.9423 (mpp) cc_final: 0.8753 (mpp) REVERT: D 983 MET cc_start: 0.8989 (tpt) cc_final: 0.8694 (tpp) REVERT: D 1161 MET cc_start: 0.9265 (tpp) cc_final: 0.8841 (tpt) REVERT: D 1208 MET cc_start: 0.9400 (pmm) cc_final: 0.8119 (pmm) REVERT: F 231 TYR cc_start: 0.9038 (t80) cc_final: 0.8812 (t80) REVERT: F 263 MET cc_start: 0.9717 (tmm) cc_final: 0.9512 (tmm) REVERT: F 281 MET cc_start: 0.9483 (ptp) cc_final: 0.9218 (ptm) REVERT: F 282 MET cc_start: 0.9737 (mmt) cc_final: 0.9444 (mmt) REVERT: F 359 MET cc_start: 0.9544 (mtp) cc_final: 0.9327 (mtp) REVERT: F 403 MET cc_start: 0.9007 (mmp) cc_final: 0.8804 (mmm) REVERT: F 511 MET cc_start: 0.9420 (tpt) cc_final: 0.9107 (tpt) outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.1762 time to fit residues: 40.8624 Evaluate side-chains 111 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 162 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 317 optimal weight: 0.0370 chunk 269 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 HIS ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.027512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.019621 restraints weight = 295007.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.020338 restraints weight = 185244.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.020861 restraints weight = 133461.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.021256 restraints weight = 104311.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.021499 restraints weight = 86495.377| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27761 Z= 0.214 Angle : 0.686 15.320 37840 Z= 0.354 Chirality : 0.044 0.301 4305 Planarity : 0.005 0.060 4789 Dihedral : 15.763 177.303 4348 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 3331 helix: 0.60 (0.14), residues: 1294 sheet: -2.00 (0.27), residues: 340 loop : -1.78 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG F 384 TYR 0.025 0.002 TYR E 56 PHE 0.017 0.002 PHE D 452 TRP 0.014 0.002 TRP J 82 HIS 0.010 0.002 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (27754) covalent geometry : angle 0.68312 / 0.35 (37834) hydrogen bonds : bond 0.04586 / 3.10 ( 1192) hydrogen bonds : angle 5.38147 / 3.66 ( 3335) metal coordination : bond 0.00978 / 0.83 ( 6) metal coordination : angle 4.78379 / 2.36 ( 6) Misc. bond : bond 0.00275 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8216 (tpp) cc_final: 0.7695 (mtt) REVERT: B 96 TYR cc_start: 0.8787 (m-80) cc_final: 0.8245 (m-80) REVERT: C 103 MET cc_start: 0.8998 (mmm) cc_final: 0.8632 (mmm) REVERT: C 159 MET cc_start: 0.9036 (mmm) cc_final: 0.8544 (mmm) REVERT: C 440 MET cc_start: 0.9053 (tmm) cc_final: 0.8652 (tmm) REVERT: C 579 MET cc_start: 0.9189 (tpt) cc_final: 0.8962 (tpt) REVERT: C 586 MET cc_start: 0.8868 (pmm) cc_final: 0.8600 (pmm) REVERT: C 607 MET cc_start: 0.9672 (mmp) cc_final: 0.9212 (mmm) REVERT: C 611 MET cc_start: 0.9708 (mtm) cc_final: 0.9072 (mtp) REVERT: C 661 MET cc_start: 0.8913 (tpt) cc_final: 0.8581 (tpt) REVERT: C 713 MET cc_start: 0.8591 (mmm) cc_final: 0.8216 (mmm) REVERT: C 724 MET cc_start: 0.9551 (ptm) cc_final: 0.9180 (tmm) REVERT: C 741 LEU cc_start: 0.9705 (mt) cc_final: 0.9498 (tt) REVERT: C 783 ASP cc_start: 0.9443 (m-30) cc_final: 0.9168 (p0) REVERT: C 1028 MET cc_start: 0.9073 (tmm) cc_final: 0.8847 (tmm) REVERT: C 1068 PHE cc_start: 0.8999 (t80) cc_final: 0.8679 (t80) REVERT: C 1076 MET cc_start: 0.9007 (ttt) cc_final: 0.8748 (ttt) REVERT: C 1127 GLU cc_start: 0.9716 (mt-10) cc_final: 0.9476 (mt-10) REVERT: D 120 LEU cc_start: 0.9183 (mp) cc_final: 0.8930 (tp) REVERT: D 143 MET cc_start: 0.8973 (ttm) cc_final: 0.8548 (ttm) REVERT: D 373 MET cc_start: 0.9389 (mtp) cc_final: 0.9018 (mtp) REVERT: D 379 ASP cc_start: 0.9389 (m-30) cc_final: 0.9159 (m-30) REVERT: D 447 MET cc_start: 0.9279 (ttt) cc_final: 0.9040 (ttt) REVERT: D 457 MET cc_start: 0.9566 (mtt) cc_final: 0.9249 (mmm) REVERT: D 559 MET cc_start: 0.9444 (mpp) cc_final: 0.8791 (mpp) REVERT: D 983 MET cc_start: 0.9061 (tpt) cc_final: 0.8699 (tpp) REVERT: D 1161 MET cc_start: 0.9269 (tpp) cc_final: 0.8863 (tpt) REVERT: D 1208 MET cc_start: 0.9376 (pmm) cc_final: 0.8096 (pmm) REVERT: F 231 TYR cc_start: 0.9072 (t80) cc_final: 0.8838 (t80) REVERT: F 263 MET cc_start: 0.9719 (tmm) cc_final: 0.9510 (tmm) REVERT: F 281 MET cc_start: 0.9461 (ptp) cc_final: 0.9193 (ptm) REVERT: F 282 MET cc_start: 0.9726 (mmt) cc_final: 0.9462 (mmt) REVERT: F 343 PHE cc_start: 0.9160 (t80) cc_final: 0.8913 (t80) REVERT: F 359 MET cc_start: 0.9569 (mtp) cc_final: 0.9312 (mtp) REVERT: F 403 MET cc_start: 0.9015 (mmp) cc_final: 0.8794 (mmm) REVERT: F 511 MET cc_start: 0.9411 (tpt) cc_final: 0.9074 (tpt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1749 time to fit residues: 39.1643 Evaluate side-chains 107 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 332 optimal weight: 30.0000 chunk 180 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 chunk 16 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 overall best weight: 2.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** 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 = 0.2732 r_free = 0.2732 target = 0.027990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.020034 restraints weight = 295631.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.020770 restraints weight = 184697.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.021309 restraints weight = 132262.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.021702 restraints weight = 102931.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.022000 restraints weight = 85372.688| |-----------------------------------------------------------------------------| r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27761 Z= 0.140 Angle : 0.645 12.297 37840 Z= 0.332 Chirality : 0.044 0.306 4305 Planarity : 0.004 0.058 4789 Dihedral : 15.659 177.307 4348 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.08 (0.15), residues: 3331 helix: 0.78 (0.14), residues: 1286 sheet: -1.86 (0.27), residues: 353 loop : -1.68 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 384 TYR 0.028 0.001 TYR E 56 PHE 0.014 0.001 PHE D 452 TRP 0.016 0.001 TRP J 82 HIS 0.008 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (27754) covalent geometry : angle 0.64299 / 0.33 (37834) hydrogen bonds : bond 0.04256 / 2.87 ( 1192) hydrogen bonds : angle 5.20609 / 3.54 ( 3335) metal coordination : bond 0.00712 / 0.62 ( 6) metal coordination : angle 4.13999 / 2.01 ( 6) Misc. bond : bond 0.00125 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8118 (tpp) cc_final: 0.7637 (mtt) REVERT: B 96 TYR cc_start: 0.8735 (m-80) cc_final: 0.8194 (m-80) REVERT: C 103 MET cc_start: 0.9070 (mmm) cc_final: 0.8718 (mmm) REVERT: C 159 MET cc_start: 0.9009 (mmm) cc_final: 0.8526 (mmm) REVERT: C 440 MET cc_start: 0.9021 (tmm) cc_final: 0.8807 (tmm) REVERT: C 607 MET cc_start: 0.9671 (mmp) cc_final: 0.9202 (mmm) REVERT: C 611 MET cc_start: 0.9685 (mtm) cc_final: 0.9040 (mtp) REVERT: C 661 MET cc_start: 0.9017 (tpt) cc_final: 0.8725 (tpt) REVERT: C 713 MET cc_start: 0.8551 (mmm) cc_final: 0.8210 (mmm) REVERT: C 724 MET cc_start: 0.9509 (ptm) cc_final: 0.9131 (tmm) REVERT: C 741 LEU cc_start: 0.9689 (mt) cc_final: 0.9475 (tt) REVERT: C 783 ASP cc_start: 0.9327 (m-30) cc_final: 0.9070 (p0) REVERT: C 1068 PHE cc_start: 0.8999 (t80) cc_final: 0.8652 (t80) REVERT: C 1076 MET cc_start: 0.8948 (ttt) cc_final: 0.8692 (ttt) REVERT: C 1127 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9451 (mt-10) REVERT: D 120 LEU cc_start: 0.9112 (mp) cc_final: 0.8894 (tp) REVERT: D 143 MET cc_start: 0.8998 (ttm) cc_final: 0.8597 (ttm) REVERT: D 373 MET cc_start: 0.9405 (mtp) cc_final: 0.9009 (mtp) REVERT: D 379 ASP cc_start: 0.9367 (m-30) cc_final: 0.9142 (m-30) REVERT: D 447 MET cc_start: 0.9210 (ttt) cc_final: 0.8954 (ttt) REVERT: D 457 MET cc_start: 0.9574 (mtt) cc_final: 0.9240 (mmm) REVERT: D 559 MET cc_start: 0.9436 (mpp) cc_final: 0.8778 (mpp) REVERT: D 1161 MET cc_start: 0.9214 (tpp) cc_final: 0.8835 (tpt) REVERT: D 1208 MET cc_start: 0.9417 (pmm) cc_final: 0.8282 (pmm) REVERT: F 231 TYR cc_start: 0.9030 (t80) cc_final: 0.8793 (t80) REVERT: F 263 MET cc_start: 0.9716 (tmm) cc_final: 0.9499 (tmm) REVERT: F 281 MET cc_start: 0.9453 (ptp) cc_final: 0.9193 (ptm) REVERT: F 282 MET cc_start: 0.9718 (mmt) cc_final: 0.9468 (mmt) REVERT: F 359 MET cc_start: 0.9560 (mtp) cc_final: 0.9312 (mtp) REVERT: F 511 MET cc_start: 0.9407 (tpt) cc_final: 0.9137 (tpt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1754 time to fit residues: 40.0062 Evaluate side-chains 111 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 331 optimal weight: 50.0000 chunk 279 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** F 516 HIS ** 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 = 0.2733 r_free = 0.2733 target = 0.028053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.020084 restraints weight = 291514.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.020818 restraints weight = 181861.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.021356 restraints weight = 130214.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.021739 restraints weight = 101689.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.022048 restraints weight = 84421.752| |-----------------------------------------------------------------------------| r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27761 Z= 0.135 Angle : 0.633 12.609 37840 Z= 0.326 Chirality : 0.044 0.304 4305 Planarity : 0.004 0.059 4789 Dihedral : 15.559 176.747 4348 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3331 helix: 0.90 (0.15), residues: 1289 sheet: -1.78 (0.26), residues: 368 loop : -1.62 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 572 TYR 0.027 0.001 TYR E 56 PHE 0.014 0.001 PHE F 453 TRP 0.016 0.001 TRP J 82 HIS 0.008 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (27754) covalent geometry : angle 0.63171 / 0.33 (37834) hydrogen bonds : bond 0.04118 / 2.79 ( 1192) hydrogen bonds : angle 5.11427 / 3.48 ( 3335) metal coordination : bond 0.00617 / 0.54 ( 6) metal coordination : angle 3.79511 / 1.80 ( 6) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8066 (tpp) cc_final: 0.7590 (mtt) REVERT: B 96 TYR cc_start: 0.8745 (m-80) cc_final: 0.8199 (m-80) REVERT: C 103 MET cc_start: 0.9007 (mmm) cc_final: 0.8668 (mmm) REVERT: C 159 MET cc_start: 0.9010 (mmm) cc_final: 0.8529 (mmm) REVERT: C 258 MET cc_start: 0.8639 (ptt) cc_final: 0.8397 (ppp) REVERT: C 440 MET cc_start: 0.8998 (tmm) cc_final: 0.8781 (tmm) REVERT: C 607 MET cc_start: 0.9669 (mmp) cc_final: 0.9116 (mmm) REVERT: C 611 MET cc_start: 0.9681 (mtm) cc_final: 0.9019 (mtt) REVERT: C 661 MET cc_start: 0.9014 (tpt) cc_final: 0.8714 (tpt) REVERT: C 713 MET cc_start: 0.8535 (mmm) cc_final: 0.8203 (mmm) REVERT: C 724 MET cc_start: 0.9488 (ptm) cc_final: 0.9102 (tmm) REVERT: C 741 LEU cc_start: 0.9692 (mt) cc_final: 0.9443 (tt) REVERT: C 783 ASP cc_start: 0.9337 (m-30) cc_final: 0.9084 (p0) REVERT: C 904 MET cc_start: 0.9298 (tpp) cc_final: 0.7915 (mtt) REVERT: C 1068 PHE cc_start: 0.9188 (t80) cc_final: 0.8915 (t80) REVERT: C 1076 MET cc_start: 0.8955 (ttt) cc_final: 0.8689 (ttt) REVERT: C 1127 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9476 (mt-10) REVERT: D 106 TYR cc_start: 0.9210 (m-10) cc_final: 0.8860 (m-10) REVERT: D 120 LEU cc_start: 0.9111 (mp) cc_final: 0.8897 (tp) REVERT: D 143 MET cc_start: 0.8992 (ttm) cc_final: 0.8579 (ttm) REVERT: D 373 MET cc_start: 0.9412 (mtp) cc_final: 0.9010 (mtp) REVERT: D 379 ASP cc_start: 0.9356 (m-30) cc_final: 0.9132 (m-30) REVERT: D 447 MET cc_start: 0.9246 (ttt) cc_final: 0.8986 (ttt) REVERT: D 457 MET cc_start: 0.9587 (mtt) cc_final: 0.9146 (mmm) REVERT: D 473 LYS cc_start: 0.9777 (tttm) cc_final: 0.9557 (mttt) REVERT: D 559 MET cc_start: 0.9418 (mpp) cc_final: 0.8796 (mpp) REVERT: D 1161 MET cc_start: 0.9201 (tpp) cc_final: 0.8851 (tpt) REVERT: D 1208 MET cc_start: 0.9406 (pmm) cc_final: 0.8253 (pmm) REVERT: F 231 TYR cc_start: 0.9043 (t80) cc_final: 0.8810 (t80) REVERT: F 263 MET cc_start: 0.9714 (tmm) cc_final: 0.9495 (tmm) REVERT: F 281 MET cc_start: 0.9461 (ptp) cc_final: 0.9212 (ptm) REVERT: F 282 MET cc_start: 0.9710 (mmt) cc_final: 0.9474 (mmt) REVERT: F 359 MET cc_start: 0.9562 (mtp) cc_final: 0.9310 (mtp) REVERT: F 511 MET cc_start: 0.9406 (tpt) cc_final: 0.9142 (tpt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1772 time to fit residues: 39.2917 Evaluate side-chains 111 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 297 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN F 516 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.028280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.020214 restraints weight = 286394.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.020954 restraints weight = 179769.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021506 restraints weight = 128533.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.021905 restraints weight = 100270.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.022153 restraints weight = 83044.633| |-----------------------------------------------------------------------------| r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27761 Z= 0.119 Angle : 0.632 12.938 37840 Z= 0.323 Chirality : 0.044 0.304 4305 Planarity : 0.004 0.059 4789 Dihedral : 15.405 176.449 4348 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.81 (0.15), residues: 3331 helix: 0.99 (0.15), residues: 1291 sheet: -1.72 (0.27), residues: 372 loop : -1.51 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 384 TYR 0.039 0.001 TYR D 793 PHE 0.012 0.001 PHE C 187 TRP 0.017 0.001 TRP J 82 HIS 0.007 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (27754) covalent geometry : angle 0.63039 / 0.32 (37834) hydrogen bonds : bond 0.03942 / 2.66 ( 1192) hydrogen bonds : angle 4.99985 / 3.40 ( 3335) metal coordination : bond 0.00510 / 0.45 ( 6) metal coordination : angle 3.53407 / 1.62 ( 6) Misc. bond : bond 0.00105 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8087 (tpp) cc_final: 0.7555 (mtt) REVERT: B 96 TYR cc_start: 0.8732 (m-80) cc_final: 0.8194 (m-80) REVERT: C 103 MET cc_start: 0.9012 (mmm) cc_final: 0.8637 (mmm) REVERT: C 159 MET cc_start: 0.9006 (mmm) cc_final: 0.8521 (mmm) REVERT: C 258 MET cc_start: 0.8683 (ptt) cc_final: 0.8467 (ppp) REVERT: C 440 MET cc_start: 0.8994 (tmm) cc_final: 0.8470 (tmm) REVERT: C 607 MET cc_start: 0.9676 (mmp) cc_final: 0.9119 (mmm) REVERT: C 611 MET cc_start: 0.9675 (mtm) cc_final: 0.9033 (mtt) REVERT: C 661 MET cc_start: 0.9033 (tpt) cc_final: 0.8723 (tpt) REVERT: C 713 MET cc_start: 0.8546 (mmm) cc_final: 0.8233 (mmm) REVERT: C 724 MET cc_start: 0.9460 (ptm) cc_final: 0.9187 (ppp) REVERT: C 741 LEU cc_start: 0.9653 (mt) cc_final: 0.9425 (tt) REVERT: C 783 ASP cc_start: 0.9323 (m-30) cc_final: 0.9099 (p0) REVERT: C 1031 MET cc_start: 0.9087 (mtm) cc_final: 0.8723 (mtp) REVERT: C 1076 MET cc_start: 0.8961 (ttt) cc_final: 0.8682 (ttt) REVERT: C 1127 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9454 (mt-10) REVERT: D 106 TYR cc_start: 0.9122 (m-10) cc_final: 0.8841 (m-10) REVERT: D 120 LEU cc_start: 0.9118 (mp) cc_final: 0.8894 (tp) REVERT: D 143 MET cc_start: 0.8993 (ttm) cc_final: 0.8565 (ttm) REVERT: D 256 MET cc_start: 0.8475 (mmm) cc_final: 0.8240 (mmt) REVERT: D 373 MET cc_start: 0.9443 (mtp) cc_final: 0.9042 (mtp) REVERT: D 379 ASP cc_start: 0.9357 (m-30) cc_final: 0.9135 (m-30) REVERT: D 447 MET cc_start: 0.9189 (ttt) cc_final: 0.8927 (ttt) REVERT: D 457 MET cc_start: 0.9585 (mtt) cc_final: 0.9183 (mmm) REVERT: D 559 MET cc_start: 0.9433 (mpp) cc_final: 0.8824 (mpp) REVERT: D 1161 MET cc_start: 0.9207 (tpp) cc_final: 0.8865 (tpt) REVERT: D 1208 MET cc_start: 0.9367 (pmm) cc_final: 0.8164 (pmm) REVERT: F 231 TYR cc_start: 0.9069 (t80) cc_final: 0.8856 (t80) REVERT: F 263 MET cc_start: 0.9716 (tmm) cc_final: 0.9447 (tmm) REVERT: F 281 MET cc_start: 0.9442 (ptp) cc_final: 0.9182 (ptm) REVERT: F 282 MET cc_start: 0.9701 (mmt) cc_final: 0.9465 (mmt) REVERT: F 359 MET cc_start: 0.9502 (mtp) cc_final: 0.9264 (mtp) REVERT: F 511 MET cc_start: 0.9451 (tpt) cc_final: 0.9235 (tpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1767 time to fit residues: 39.4850 Evaluate side-chains 113 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 115 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 325 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.028109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.020128 restraints weight = 289759.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.020855 restraints weight = 181474.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.021395 restraints weight = 130189.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.021798 restraints weight = 101453.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.022078 restraints weight = 84219.661| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27761 Z= 0.139 Angle : 0.629 12.923 37840 Z= 0.323 Chirality : 0.043 0.302 4305 Planarity : 0.004 0.058 4789 Dihedral : 15.345 177.007 4348 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.15), residues: 3331 helix: 1.09 (0.15), residues: 1288 sheet: -1.63 (0.27), residues: 369 loop : -1.47 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 384 TYR 0.025 0.001 TYR E 56 PHE 0.012 0.001 PHE D 452 TRP 0.014 0.001 TRP J 82 HIS 0.007 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (27754) covalent geometry : angle 0.62715 / 0.32 (37834) hydrogen bonds : bond 0.04002 / 2.70 ( 1192) hydrogen bonds : angle 4.97273 / 3.40 ( 3335) metal coordination : bond 0.00629 / 0.54 ( 6) metal coordination : angle 3.42542 / 1.58 ( 6) Misc. bond : bond 0.00105 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.47 seconds wall clock time: 63 minutes 17.35 seconds (3797.35 seconds total)