Starting phenix.real_space_refine on Mon Aug 25 07:06:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.map" model { file = "/net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e74_27935/08_2025/8e74_27935.cif" } resolution = 2.94 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= 0.003 sd= 0.170 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 106 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 15861 2.51 5 N 4565 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25815 Number of models: 1 Model: "" Number of chains: 10 Chain: "Z" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8600 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1047} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9920 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 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: "O" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 751 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 678 Classifications: {'RNA': 32} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 29} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13556 SG CYS D 60 21.001 35.712 111.958 1.00 80.49 S ATOM 13574 SG CYS D 62 20.954 34.463 115.063 1.00 85.19 S ATOM 13683 SG CYS D 75 18.042 36.677 115.004 1.00 85.24 S ATOM 13709 SG CYS D 78 21.654 37.288 115.288 1.00 78.29 S ATOM 20124 SG CYS D 891 36.009 98.501 87.474 1.00 52.24 S ATOM 20691 SG CYS D 968 38.045 95.031 88.631 1.00 47.29 S ATOM 20733 SG CYS D 975 36.802 95.312 85.263 1.00 56.83 S ATOM 20751 SG CYS D 978 38.977 97.414 85.723 1.00 44.58 S Time building chain proxies: 6.26, per 1000 atoms: 0.24 Number of scatterers: 25815 At special positions: 0 Unit cell: (125.57, 128.817, 199.18, 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 88 16.00 P 106 15.00 Mg 1 11.99 O 5192 8.00 N 4565 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 42 sheets defined 39.7% alpha, 17.7% beta 43 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'Z' and resid 33 through 45 removed outlier: 3.850A pdb=" N SER Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS Z 45 " --> pdb=" O GLU Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 73 removed outlier: 4.044A pdb=" N GLN Z 71 " --> pdb=" O GLU Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 96 Processing helix chain 'Z' and resid 116 through 125 removed outlier: 3.848A pdb=" N ALA Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 151 Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.541A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.176A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.061A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.515A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (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: 3.845A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.967A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.679A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.606A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.645A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.699A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.633A pdb=" N ILE C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.618A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.685A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.062A pdb=" N ALA C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.852A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.525A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.592A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.826A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.963A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 removed outlier: 3.535A pdb=" N ILE C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.749A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.506A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.613A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.290A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.954A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.750A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 187 removed outlier: 3.618A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.644A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.622A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.660A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.987A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.614A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.919A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.582A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.530A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.554A pdb=" N ARG D 459 " --> pdb=" O PHE D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.254A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.583A pdb=" N ALA D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.594A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.606A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.754A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.167A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (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 975 through 980 removed outlier: 3.541A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.526A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.696A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.525A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.325A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.878A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.751A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.549A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'Z' and resid 79 through 83 removed outlier: 3.533A pdb=" N GLN Z 81 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL Z 51 " --> pdb=" O PHE Z 132 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE Z 132 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS Z 53 " --> pdb=" O THR Z 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 86 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 12 removed outlier: 5.844A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.572A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.601A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.635A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.330A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) 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 removed outlier: 3.540A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.451A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) 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 96 through 97 removed outlier: 4.071A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.294A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.455A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 215 " --> pdb=" O GLY C 223 " (cutoff:3.500A) 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 505 through 506 removed outlier: 5.179A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.548A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.414A 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 671 removed outlier: 6.667A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.703A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.724A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.518A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 784 through 785 removed outlier: 5.162A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.818A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD5, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD6, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.747A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.597A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.513A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 328 through 330 removed outlier: 3.659A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.391A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.956A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 6.262A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.785A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 1003 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.39 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7632 1.33 - 1.45: 3931 1.45 - 1.57: 14552 1.57 - 1.69: 208 1.69 - 1.81: 155 Bond restraints: 26478 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" CB ASP C 903 " pdb=" CG ASP C 903 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.38e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CA GLY C 608 " pdb=" C GLY C 608 " ideal model delta sigma weight residual 1.516 1.500 0.016 1.12e-02 7.97e+03 2.06e+00 ... (remaining 26473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 34933 1.46 - 2.92: 1198 2.92 - 4.39: 207 4.39 - 5.85: 7 5.85 - 7.31: 3 Bond angle restraints: 36348 Sorted by residual: angle pdb=" C PRO B 28 " pdb=" N GLY B 29 " pdb=" CA GLY B 29 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" N ILE B 159 " pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N VAL C 780 " pdb=" CA VAL C 780 " pdb=" C VAL C 780 " ideal model delta sigma weight residual 111.91 109.01 2.90 8.90e-01 1.26e+00 1.06e+01 angle pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 113.12 109.05 4.07 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N GLY D 508 " pdb=" CA GLY D 508 " pdb=" C GLY D 508 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.28e+00 ... (remaining 36343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 15294 34.30 - 68.59: 692 68.59 - 102.89: 38 102.89 - 137.19: 0 137.19 - 171.48: 5 Dihedral angle restraints: 16029 sinusoidal: 7309 harmonic: 8720 Sorted by residual: dihedral pdb=" CA ARG C 563 " pdb=" C ARG C 563 " pdb=" N LYS C 564 " pdb=" CA LYS C 564 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ALA C 766 " pdb=" C ALA C 766 " pdb=" N GLU C 767 " pdb=" CA GLU C 767 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DA P 118 " pdb=" C3' DA P 118 " pdb=" O3' DA P 118 " pdb=" P DA P 119 " ideal model delta sinusoidal sigma weight residual 220.00 48.52 171.48 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2710 0.034 - 0.069: 1011 0.069 - 0.103: 297 0.103 - 0.137: 147 0.137 - 0.172: 7 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE C1112 " pdb=" N ILE C1112 " pdb=" C ILE C1112 " pdb=" CB ILE C1112 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE D1149 " pdb=" N ILE D1149 " pdb=" C ILE D1149 " pdb=" CB ILE D1149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 4169 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 144 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C ARG D 144 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG D 144 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS D 145 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D 434 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO D 658 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " -0.024 5.00e-02 4.00e+02 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 30 2.31 - 2.96: 11987 2.96 - 3.61: 35937 3.61 - 4.25: 59233 4.25 - 4.90: 100247 Nonbonded interactions: 207434 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.665 2.170 nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 1.873 2.170 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 2.005 3.040 nonbonded pdb=" O ASP C 761 " pdb=" OG1 THR C 762 " model vdw 2.030 3.040 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.049 2.170 ... (remaining 207429 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26486 Z= 0.202 Angle : 0.719 33.900 36360 Z= 0.391 Chirality : 0.043 0.172 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.975 171.483 10425 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 2.63 % Allowed : 9.89 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 3032 helix: 0.19 (0.16), residues: 1107 sheet: -0.81 (0.26), residues: 416 loop : -1.44 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 478 TYR 0.016 0.001 TYR A 168 PHE 0.013 0.001 PHE C 906 TRP 0.011 0.001 TRP D 723 HIS 0.005 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00440 (26478) covalent geometry : angle 0.64469 (36348) hydrogen bonds : bond 0.17975 ( 1087) hydrogen bonds : angle 6.70874 ( 3007) metal coordination : bond 0.03040 ( 8) metal coordination : angle 17.49555 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 125 ASN cc_start: 0.8532 (m-40) cc_final: 0.8287 (m-40) REVERT: A 137 GLU cc_start: 0.7885 (pp20) cc_final: 0.7664 (pp20) REVERT: B 177 LYS cc_start: 0.8144 (mttp) cc_final: 0.7801 (tttp) REVERT: C 336 GLU cc_start: 0.6677 (tp30) cc_final: 0.6427 (tp30) REVERT: C 393 MET cc_start: 0.8583 (mmt) cc_final: 0.8150 (mmt) REVERT: C 429 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6649 (tp30) REVERT: C 440 MET cc_start: 0.9028 (ttt) cc_final: 0.8612 (ttt) REVERT: C 529 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 733 ASP cc_start: 0.8435 (m-30) cc_final: 0.8139 (m-30) REVERT: C 758 ASP cc_start: 0.8160 (p0) cc_final: 0.7821 (p0) REVERT: C 760 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7362 (mtt90) REVERT: C 814 LEU cc_start: 0.1939 (OUTLIER) cc_final: 0.1247 (mm) REVERT: C 903 ASP cc_start: 0.8538 (p0) cc_final: 0.8333 (p0) REVERT: C 947 ASP cc_start: 0.7765 (p0) cc_final: 0.7315 (p0) REVERT: D 123 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8043 (mptp) REVERT: D 177 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.3689 (mp) REVERT: D 530 GLU cc_start: 0.7613 (tt0) cc_final: 0.7215 (pm20) REVERT: D 733 MET cc_start: 0.8912 (ptt) cc_final: 0.8640 (ptm) REVERT: D 796 ASP cc_start: 0.8282 (p0) cc_final: 0.8025 (p0) REVERT: D 1265 ASN cc_start: 0.8485 (m-40) cc_final: 0.8094 (m-40) outliers start: 67 outliers final: 31 residues processed: 357 average time/residue: 0.6841 time to fit residues: 280.2650 Evaluate side-chains 295 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 136 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 53 HIS A 100 GLN B 5 GLN B 79 ASN C 476 HIS C 603 ASN D 5 ASN D 239 ASN E 100 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120695 restraints weight = 26274.098| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.72 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26486 Z= 0.155 Angle : 0.609 10.685 36360 Z= 0.321 Chirality : 0.044 0.189 4172 Planarity : 0.005 0.043 4401 Dihedral : 17.131 179.620 4702 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer: Outliers : 3.06 % Allowed : 12.40 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 3032 helix: 0.79 (0.16), residues: 1095 sheet: -0.30 (0.25), residues: 418 loop : -1.30 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.015 0.001 TYR A 168 PHE 0.012 0.001 PHE C 906 TRP 0.012 0.001 TRP C 938 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00352 (26478) covalent geometry : angle 0.60347 (36348) hydrogen bonds : bond 0.05520 ( 1087) hydrogen bonds : angle 4.89126 ( 3007) metal coordination : bond 0.00656 ( 8) metal coordination : angle 4.35635 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 299 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6396 (pp20) REVERT: Z 125 ASN cc_start: 0.8566 (m-40) cc_final: 0.8287 (m-40) REVERT: A 137 GLU cc_start: 0.8116 (pp20) cc_final: 0.7815 (pp20) REVERT: B 2 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 52 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 188 ASP cc_start: 0.8377 (t0) cc_final: 0.8083 (t0) REVERT: B 224 GLU cc_start: 0.7142 (pp20) cc_final: 0.6838 (pp20) REVERT: C 336 GLU cc_start: 0.6824 (tp30) cc_final: 0.6539 (tp30) REVERT: C 429 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6695 (tp30) REVERT: C 584 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6917 (ptp-110) REVERT: C 733 ASP cc_start: 0.8570 (m-30) cc_final: 0.8268 (m-30) REVERT: C 758 ASP cc_start: 0.8555 (p0) cc_final: 0.8235 (p0) REVERT: C 814 LEU cc_start: 0.1012 (OUTLIER) cc_final: 0.0552 (mm) REVERT: C 843 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 853 PHE cc_start: 0.8110 (m-80) cc_final: 0.7803 (m-80) REVERT: C 947 ASP cc_start: 0.7784 (p0) cc_final: 0.7408 (p0) REVERT: D 177 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.3959 (mp) REVERT: D 215 GLU cc_start: 0.6354 (mp0) cc_final: 0.6124 (mp0) REVERT: D 377 SER cc_start: 0.8523 (m) cc_final: 0.8289 (p) REVERT: D 530 GLU cc_start: 0.7889 (tt0) cc_final: 0.6997 (pm20) REVERT: D 541 MET cc_start: 0.9119 (mtm) cc_final: 0.8825 (mtm) REVERT: D 733 MET cc_start: 0.8837 (ptt) cc_final: 0.8615 (ptm) REVERT: D 744 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6893 (mt-10) REVERT: D 796 ASP cc_start: 0.8135 (p0) cc_final: 0.7924 (p0) REVERT: D 1265 ASN cc_start: 0.8345 (m-40) cc_final: 0.7897 (m110) REVERT: E 36 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8372 (p) outliers start: 78 outliers final: 46 residues processed: 351 average time/residue: 0.6016 time to fit residues: 243.7841 Evaluate side-chains 312 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 39 optimal weight: 0.0470 chunk 219 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 209 optimal weight: 0.0060 chunk 15 optimal weight: 0.8980 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 407 GLN C 603 ASN C1066 GLN D 239 ASN D1125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124009 restraints weight = 26283.370| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.76 r_work: 0.3187 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26486 Z= 0.112 Angle : 0.536 9.868 36360 Z= 0.286 Chirality : 0.041 0.175 4172 Planarity : 0.004 0.045 4401 Dihedral : 16.888 179.286 4690 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.83 % Favored : 95.84 % Rotamer: Outliers : 3.73 % Allowed : 12.91 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 3032 helix: 1.23 (0.16), residues: 1081 sheet: -0.19 (0.25), residues: 413 loop : -1.12 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 173 TYR 0.010 0.001 TYR D1142 PHE 0.022 0.001 PHE D 6 TRP 0.011 0.001 TRP D 723 HIS 0.003 0.000 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00236 (26478) covalent geometry : angle 0.53371 (36348) hydrogen bonds : bond 0.04416 ( 1087) hydrogen bonds : angle 4.45213 ( 3007) metal coordination : bond 0.00420 ( 8) metal coordination : angle 2.88342 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 321 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6378 (pp20) REVERT: A 84 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 89 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: A 137 GLU cc_start: 0.8110 (pp20) cc_final: 0.7795 (pp20) REVERT: B 188 ASP cc_start: 0.8341 (t0) cc_final: 0.8093 (t0) REVERT: B 224 GLU cc_start: 0.7127 (pp20) cc_final: 0.6737 (pp20) REVERT: C 114 ASP cc_start: 0.8494 (m-30) cc_final: 0.8118 (m-30) REVERT: C 259 ARG cc_start: 0.7141 (mmm-85) cc_final: 0.6785 (mpp80) REVERT: C 336 GLU cc_start: 0.6700 (tp30) cc_final: 0.6382 (tp30) REVERT: C 393 MET cc_start: 0.8694 (mmt) cc_final: 0.8279 (mmt) REVERT: C 429 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6739 (tp30) REVERT: C 467 ARG cc_start: 0.6997 (mpt-90) cc_final: 0.6644 (mpt-90) REVERT: C 534 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: C 584 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6871 (ptp-110) REVERT: C 622 GLU cc_start: 0.8856 (tt0) cc_final: 0.8624 (tt0) REVERT: C 645 GLU cc_start: 0.8303 (tt0) cc_final: 0.7908 (mt-10) REVERT: C 758 ASP cc_start: 0.8503 (p0) cc_final: 0.8251 (p0) REVERT: C 814 LEU cc_start: 0.0793 (OUTLIER) cc_final: 0.0408 (mm) REVERT: C 843 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7522 (mt-10) REVERT: C 867 GLU cc_start: 0.8144 (tt0) cc_final: 0.7936 (tt0) REVERT: C 947 ASP cc_start: 0.7657 (p0) cc_final: 0.7344 (p0) REVERT: C 1063 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: D 123 LYS cc_start: 0.8275 (mptp) cc_final: 0.8002 (mmtm) REVERT: D 177 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.3772 (mp) REVERT: D 215 GLU cc_start: 0.6368 (mp0) cc_final: 0.6153 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6732 (OUTLIER) cc_final: 0.6391 (m) REVERT: D 356 ARG cc_start: 0.7630 (ttt90) cc_final: 0.6785 (ttp-110) REVERT: D 541 MET cc_start: 0.9063 (mtm) cc_final: 0.8841 (mtm) REVERT: D 791 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: D 796 ASP cc_start: 0.8076 (p0) cc_final: 0.7766 (p0) REVERT: D 1117 ASP cc_start: 0.7868 (p0) cc_final: 0.7595 (p0) REVERT: D 1265 ASN cc_start: 0.8278 (m-40) cc_final: 0.7838 (m-40) REVERT: E 66 ASP cc_start: 0.7875 (m-30) cc_final: 0.7363 (m-30) outliers start: 95 outliers final: 43 residues processed: 387 average time/residue: 0.6612 time to fit residues: 296.0001 Evaluate side-chains 328 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 124 ARG Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 117 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 241 optimal weight: 0.0060 chunk 263 optimal weight: 5.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 545 ASN C 603 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118468 restraints weight = 26187.391| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.81 r_work: 0.3103 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26486 Z= 0.221 Angle : 0.626 13.088 36360 Z= 0.328 Chirality : 0.046 0.226 4172 Planarity : 0.005 0.047 4401 Dihedral : 16.942 179.301 4681 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 4.16 % Allowed : 14.40 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3032 helix: 1.03 (0.16), residues: 1091 sheet: -0.18 (0.25), residues: 425 loop : -1.19 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 350 TYR 0.020 0.002 TYR A 168 PHE 0.019 0.002 PHE C 906 TRP 0.012 0.002 TRP C 938 HIS 0.006 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00544 (26478) covalent geometry : angle 0.62423 (36348) hydrogen bonds : bond 0.05759 ( 1087) hydrogen bonds : angle 4.55889 ( 3007) metal coordination : bond 0.00516 ( 8) metal coordination : angle 2.95893 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 274 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8547 (t) REVERT: A 89 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: A 137 GLU cc_start: 0.8078 (pp20) cc_final: 0.7747 (pp20) REVERT: B 2 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7843 (mm) REVERT: B 34 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8156 (pt) REVERT: B 177 LYS cc_start: 0.8112 (mttp) cc_final: 0.7622 (tttp) REVERT: B 188 ASP cc_start: 0.8421 (t0) cc_final: 0.8077 (t0) REVERT: B 224 GLU cc_start: 0.7322 (pp20) cc_final: 0.6893 (pp20) REVERT: C 252 PHE cc_start: 0.8402 (m-80) cc_final: 0.8158 (m-80) REVERT: C 393 MET cc_start: 0.8718 (mmt) cc_final: 0.8354 (mmt) REVERT: C 429 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6818 (tp30) REVERT: C 440 MET cc_start: 0.8985 (ttt) cc_final: 0.8595 (ttt) REVERT: C 467 ARG cc_start: 0.7276 (mpt-90) cc_final: 0.6686 (mpt-90) REVERT: C 584 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6998 (ptp-110) REVERT: C 758 ASP cc_start: 0.8576 (p0) cc_final: 0.8282 (p0) REVERT: C 814 LEU cc_start: 0.0844 (OUTLIER) cc_final: 0.0513 (mm) REVERT: C 843 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 885 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 947 ASP cc_start: 0.7739 (p0) cc_final: 0.7376 (p0) REVERT: C 982 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 1063 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: D 39 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7352 (mp) REVERT: D 123 LYS cc_start: 0.8373 (mptp) cc_final: 0.8022 (mmtm) REVERT: D 177 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.3689 (mp) REVERT: D 215 GLU cc_start: 0.6438 (mp0) cc_final: 0.6228 (OUTLIER) REVERT: D 236 VAL cc_start: 0.6932 (OUTLIER) cc_final: 0.6607 (m) REVERT: D 243 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7472 (mt-10) REVERT: D 339 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7384 (t0) REVERT: D 356 ARG cc_start: 0.7717 (ttt90) cc_final: 0.6726 (ttp-110) REVERT: D 796 ASP cc_start: 0.8017 (p0) cc_final: 0.7727 (p0) REVERT: D 1076 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7664 (p) REVERT: D 1112 MET cc_start: 0.8062 (mmm) cc_final: 0.7747 (mtp) REVERT: D 1117 ASP cc_start: 0.7904 (p0) cc_final: 0.7672 (p0) REVERT: D 1265 ASN cc_start: 0.8333 (m-40) cc_final: 0.7895 (m110) REVERT: E 70 GLN cc_start: 0.4999 (OUTLIER) cc_final: 0.4224 (tm-30) outliers start: 106 outliers final: 60 residues processed: 352 average time/residue: 0.6954 time to fit residues: 281.2805 Evaluate side-chains 341 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 267 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 285 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 300 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 603 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.171416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118044 restraints weight = 26104.226| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.76 r_work: 0.3100 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26486 Z= 0.196 Angle : 0.610 11.816 36360 Z= 0.321 Chirality : 0.045 0.167 4172 Planarity : 0.005 0.049 4401 Dihedral : 16.893 179.098 4672 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.58 % Favored : 95.22 % Rotamer: Outliers : 4.28 % Allowed : 15.42 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3032 helix: 0.99 (0.16), residues: 1097 sheet: -0.31 (0.25), residues: 444 loop : -1.19 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 563 TYR 0.020 0.002 TYR A 168 PHE 0.023 0.002 PHE D 70 TRP 0.013 0.002 TRP C 938 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00484 (26478) covalent geometry : angle 0.60772 (36348) hydrogen bonds : bond 0.05558 ( 1087) hydrogen bonds : angle 4.51371 ( 3007) metal coordination : bond 0.00448 ( 8) metal coordination : angle 2.78353 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 272 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 87 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5900 (pp20) REVERT: Z 102 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6693 (ttp-110) REVERT: A 84 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8591 (t) REVERT: A 137 GLU cc_start: 0.8120 (pp20) cc_final: 0.7795 (pp20) REVERT: B 34 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8139 (pt) REVERT: B 177 LYS cc_start: 0.8113 (mttp) cc_final: 0.7648 (ttpp) REVERT: B 188 ASP cc_start: 0.8418 (t0) cc_final: 0.8093 (t0) REVERT: B 224 GLU cc_start: 0.7351 (pp20) cc_final: 0.7038 (pp20) REVERT: C 121 GLU cc_start: 0.7915 (mp0) cc_final: 0.7522 (mt-10) REVERT: C 252 PHE cc_start: 0.8374 (m-80) cc_final: 0.8169 (m-80) REVERT: C 429 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6812 (tp30) REVERT: C 467 ARG cc_start: 0.7370 (mpt-90) cc_final: 0.6853 (mpt-90) REVERT: C 584 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7007 (ptp-110) REVERT: C 620 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7939 (ttp80) REVERT: C 758 ASP cc_start: 0.8506 (p0) cc_final: 0.8245 (p0) REVERT: C 814 LEU cc_start: 0.0994 (OUTLIER) cc_final: 0.0653 (mm) REVERT: C 843 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 885 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8813 (mt) REVERT: C 947 ASP cc_start: 0.7690 (p0) cc_final: 0.7338 (p0) REVERT: C 982 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: C 1063 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: D 39 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7399 (mp) REVERT: D 123 LYS cc_start: 0.8362 (mptp) cc_final: 0.7856 (mmtm) REVERT: D 177 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.3622 (mm) REVERT: D 236 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6741 (m) REVERT: D 243 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7439 (mt-10) REVERT: D 339 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7350 (t0) REVERT: D 356 ARG cc_start: 0.7687 (ttt90) cc_final: 0.6754 (ttp-110) REVERT: D 796 ASP cc_start: 0.7937 (p0) cc_final: 0.7651 (p0) REVERT: D 1076 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7678 (p) REVERT: D 1112 MET cc_start: 0.7943 (mmm) cc_final: 0.7616 (mtp) REVERT: D 1113 GLU cc_start: 0.7664 (tt0) cc_final: 0.7294 (tp30) REVERT: D 1117 ASP cc_start: 0.7920 (p0) cc_final: 0.7702 (p0) REVERT: D 1265 ASN cc_start: 0.8344 (m-40) cc_final: 0.7909 (m110) REVERT: E 70 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.4156 (tm-30) outliers start: 109 outliers final: 63 residues processed: 356 average time/residue: 0.6154 time to fit residues: 253.0664 Evaluate side-chains 343 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 264 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 102 ARG Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 892 GLN Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 191 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN C 603 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121418 restraints weight = 26083.370| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.87 r_work: 0.3148 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26486 Z= 0.117 Angle : 0.535 10.187 36360 Z= 0.285 Chirality : 0.042 0.179 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.748 178.532 4672 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.02 % Favored : 95.78 % Rotamer: Outliers : 3.49 % Allowed : 16.52 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 3032 helix: 1.25 (0.16), residues: 1096 sheet: -0.08 (0.26), residues: 418 loop : -1.03 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.012 0.001 TYR A 168 PHE 0.024 0.001 PHE D 70 TRP 0.013 0.001 TRP D 723 HIS 0.002 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00256 (26478) covalent geometry : angle 0.53305 (36348) hydrogen bonds : bond 0.04388 ( 1087) hydrogen bonds : angle 4.29933 ( 3007) metal coordination : bond 0.00350 ( 8) metal coordination : angle 2.46056 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 285 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8090 (pp20) cc_final: 0.7789 (pp20) REVERT: B 188 ASP cc_start: 0.8394 (t0) cc_final: 0.8112 (t0) REVERT: B 224 GLU cc_start: 0.7267 (pp20) cc_final: 0.6856 (pp20) REVERT: C 121 GLU cc_start: 0.7850 (mp0) cc_final: 0.7472 (mt-10) REVERT: C 188 ASP cc_start: 0.8218 (p0) cc_final: 0.7892 (p0) REVERT: C 393 MET cc_start: 0.8653 (mmt) cc_final: 0.8261 (mmt) REVERT: C 429 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6772 (tp30) REVERT: C 467 ARG cc_start: 0.7076 (mpt-90) cc_final: 0.6581 (mpt-90) REVERT: C 584 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6818 (ptp-110) REVERT: C 620 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: C 645 GLU cc_start: 0.8359 (tt0) cc_final: 0.7989 (mt-10) REVERT: C 758 ASP cc_start: 0.8471 (p0) cc_final: 0.8183 (p0) REVERT: C 760 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7057 (mtp180) REVERT: C 761 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: C 843 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 885 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8808 (mt) REVERT: C 947 ASP cc_start: 0.7659 (p0) cc_final: 0.7323 (p0) REVERT: C 1063 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: D 39 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7494 (mp) REVERT: D 123 LYS cc_start: 0.8244 (mptp) cc_final: 0.7778 (mmtm) REVERT: D 236 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6586 (m) REVERT: D 339 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7305 (t0) REVERT: D 356 ARG cc_start: 0.7709 (ttt90) cc_final: 0.6758 (ttp-110) REVERT: D 791 GLU cc_start: 0.7672 (tt0) cc_final: 0.7445 (tm-30) REVERT: D 1076 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7698 (p) REVERT: D 1087 ARG cc_start: 0.7206 (tpt-90) cc_final: 0.6739 (mtp85) REVERT: D 1112 MET cc_start: 0.7816 (mmm) cc_final: 0.7147 (mtp) REVERT: D 1113 GLU cc_start: 0.7751 (tt0) cc_final: 0.7321 (tp30) REVERT: D 1117 ASP cc_start: 0.7783 (p0) cc_final: 0.7492 (p0) REVERT: D 1137 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: D 1265 ASN cc_start: 0.8254 (m-40) cc_final: 0.7826 (m-40) outliers start: 89 outliers final: 47 residues processed: 353 average time/residue: 0.6446 time to fit residues: 262.6557 Evaluate side-chains 324 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 306 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 188 optimal weight: 6.9990 chunk 219 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN C1066 GLN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121425 restraints weight = 26113.856| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.77 r_work: 0.3152 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26486 Z= 0.124 Angle : 0.540 9.818 36360 Z= 0.286 Chirality : 0.042 0.174 4172 Planarity : 0.004 0.049 4401 Dihedral : 16.708 178.046 4668 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 3.45 % Allowed : 16.79 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3032 helix: 1.35 (0.16), residues: 1094 sheet: -0.05 (0.25), residues: 423 loop : -0.98 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.013 0.001 TYR A 168 PHE 0.025 0.001 PHE D 70 TRP 0.011 0.001 TRP D 723 HIS 0.002 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00284 (26478) covalent geometry : angle 0.53798 (36348) hydrogen bonds : bond 0.04428 ( 1087) hydrogen bonds : angle 4.21500 ( 3007) metal coordination : bond 0.00354 ( 8) metal coordination : angle 2.32581 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 282 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8117 (pp20) cc_final: 0.7800 (pp20) REVERT: B 2 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 55 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6673 (ptp90) REVERT: B 177 LYS cc_start: 0.8041 (mttp) cc_final: 0.7616 (tttp) REVERT: B 188 ASP cc_start: 0.8351 (t0) cc_final: 0.8148 (t0) REVERT: B 224 GLU cc_start: 0.7281 (pp20) cc_final: 0.6874 (pp20) REVERT: C 188 ASP cc_start: 0.8017 (p0) cc_final: 0.7724 (p0) REVERT: C 393 MET cc_start: 0.8731 (mmt) cc_final: 0.8299 (mmt) REVERT: C 429 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6778 (tp30) REVERT: C 467 ARG cc_start: 0.7094 (mpt-90) cc_final: 0.6606 (mpt-90) REVERT: C 534 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: C 535 GLU cc_start: 0.8015 (mp0) cc_final: 0.7687 (mp0) REVERT: C 584 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6848 (ptp-110) REVERT: C 620 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7831 (ttp80) REVERT: C 645 GLU cc_start: 0.8378 (tt0) cc_final: 0.8016 (mt-10) REVERT: C 758 ASP cc_start: 0.8525 (p0) cc_final: 0.8214 (p0) REVERT: C 760 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: C 761 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: C 843 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 885 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 947 ASP cc_start: 0.7679 (p0) cc_final: 0.7335 (p0) REVERT: C 982 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: C 1063 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: D 39 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7550 (mp) REVERT: D 123 LYS cc_start: 0.8286 (mptp) cc_final: 0.7791 (mmtm) REVERT: D 236 VAL cc_start: 0.6843 (OUTLIER) cc_final: 0.6536 (m) REVERT: D 239 ASN cc_start: 0.7710 (m-40) cc_final: 0.7492 (m110) REVERT: D 243 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7552 (mt-10) REVERT: D 339 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7292 (t0) REVERT: D 356 ARG cc_start: 0.7734 (ttt90) cc_final: 0.6777 (ttp-110) REVERT: D 791 GLU cc_start: 0.7633 (tt0) cc_final: 0.7395 (tm-30) REVERT: D 1076 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7730 (p) REVERT: D 1112 MET cc_start: 0.7792 (mmm) cc_final: 0.7250 (mtp) REVERT: D 1113 GLU cc_start: 0.7701 (tt0) cc_final: 0.7259 (tp30) REVERT: D 1117 ASP cc_start: 0.7793 (p0) cc_final: 0.7493 (p0) REVERT: D 1137 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: D 1265 ASN cc_start: 0.8233 (m-40) cc_final: 0.7803 (m-40) outliers start: 88 outliers final: 51 residues processed: 350 average time/residue: 0.6290 time to fit residues: 252.4831 Evaluate side-chains 336 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 120 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 90 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 264 optimal weight: 0.1980 chunk 192 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 GLN B 200 ASN C 232 GLN C 415 GLN C1066 GLN D 854 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123400 restraints weight = 26330.363| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.75 r_work: 0.3183 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26486 Z= 0.104 Angle : 0.519 10.308 36360 Z= 0.275 Chirality : 0.041 0.150 4172 Planarity : 0.004 0.047 4401 Dihedral : 16.607 177.566 4668 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 2.82 % Allowed : 17.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3032 helix: 1.53 (0.16), residues: 1097 sheet: 0.04 (0.26), residues: 417 loop : -0.89 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.011 0.001 TYR E 67 PHE 0.026 0.001 PHE D 70 TRP 0.012 0.001 TRP C 70 HIS 0.002 0.000 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00223 (26478) covalent geometry : angle 0.51718 (36348) hydrogen bonds : bond 0.03841 ( 1087) hydrogen bonds : angle 4.08026 ( 3007) metal coordination : bond 0.00323 ( 8) metal coordination : angle 2.30916 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 296 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8100 (pp20) cc_final: 0.7763 (pp20) REVERT: B 2 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7937 (mm) REVERT: B 55 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6449 (ptp90) REVERT: B 109 ASP cc_start: 0.7809 (m-30) cc_final: 0.7583 (m-30) REVERT: B 224 GLU cc_start: 0.7207 (pp20) cc_final: 0.6824 (pp20) REVERT: C 188 ASP cc_start: 0.7769 (p0) cc_final: 0.7542 (p0) REVERT: C 252 PHE cc_start: 0.8321 (m-80) cc_final: 0.8095 (m-80) REVERT: C 282 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6663 (mmt-90) REVERT: C 303 GLU cc_start: 0.7241 (pm20) cc_final: 0.6184 (tp30) REVERT: C 393 MET cc_start: 0.8620 (mmt) cc_final: 0.8217 (mmt) REVERT: C 429 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6748 (tp30) REVERT: C 467 ARG cc_start: 0.6783 (mpt-90) cc_final: 0.6413 (mpt-90) REVERT: C 535 GLU cc_start: 0.7937 (mp0) cc_final: 0.7737 (mp0) REVERT: C 584 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6737 (ptp-110) REVERT: C 645 GLU cc_start: 0.8305 (tt0) cc_final: 0.7980 (mt-10) REVERT: C 758 ASP cc_start: 0.8490 (p0) cc_final: 0.8151 (p0) REVERT: C 760 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7171 (mtp180) REVERT: C 843 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 885 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 947 ASP cc_start: 0.7457 (p0) cc_final: 0.7108 (p0) REVERT: C 1051 MET cc_start: 0.8566 (ttm) cc_final: 0.8334 (mtp) REVERT: C 1066 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8770 (mm110) REVERT: D 35 ASN cc_start: 0.7713 (t0) cc_final: 0.7282 (t0) REVERT: D 39 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7572 (mp) REVERT: D 123 LYS cc_start: 0.8122 (mptp) cc_final: 0.7593 (mmtm) REVERT: D 236 VAL cc_start: 0.6682 (OUTLIER) cc_final: 0.6347 (m) REVERT: D 248 TYR cc_start: 0.7228 (m-80) cc_final: 0.7011 (m-80) REVERT: D 250 GLU cc_start: 0.7001 (tp30) cc_final: 0.6599 (mm-30) REVERT: D 285 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5606 (ptpp) REVERT: D 356 ARG cc_start: 0.7654 (ttt90) cc_final: 0.6699 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (p) REVERT: D 1087 ARG cc_start: 0.6989 (mmm-85) cc_final: 0.6664 (mtp85) REVERT: D 1112 MET cc_start: 0.7680 (mmm) cc_final: 0.7452 (mtp) REVERT: D 1117 ASP cc_start: 0.7707 (p0) cc_final: 0.7383 (p0) REVERT: D 1137 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 1265 ASN cc_start: 0.8127 (m-40) cc_final: 0.7713 (m-40) REVERT: E 66 ASP cc_start: 0.7769 (m-30) cc_final: 0.7342 (m-30) outliers start: 72 outliers final: 40 residues processed: 351 average time/residue: 0.6648 time to fit residues: 269.5107 Evaluate side-chains 332 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1066 GLN Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 271 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C1066 GLN D 239 ASN D 854 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116871 restraints weight = 26317.489| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.85 r_work: 0.3070 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 26486 Z= 0.265 Angle : 0.688 14.507 36360 Z= 0.358 Chirality : 0.048 0.183 4172 Planarity : 0.006 0.056 4401 Dihedral : 16.859 177.873 4664 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer: Outliers : 3.26 % Allowed : 17.93 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.15), residues: 3032 helix: 1.06 (0.16), residues: 1086 sheet: -0.20 (0.25), residues: 433 loop : -1.08 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1067 TYR 0.026 0.002 TYR A 168 PHE 0.028 0.002 PHE D 70 TRP 0.014 0.002 TRP D 484 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00663 (26478) covalent geometry : angle 0.68626 (36348) hydrogen bonds : bond 0.06299 ( 1087) hydrogen bonds : angle 4.49133 ( 3007) metal coordination : bond 0.00454 ( 8) metal coordination : angle 2.68800 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 0.867 Fit side-chains REVERT: A 131 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8045 (mmtm) REVERT: A 137 GLU cc_start: 0.8167 (pp20) cc_final: 0.7805 (pp20) REVERT: B 55 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6521 (ptp90) REVERT: B 177 LYS cc_start: 0.8136 (mttp) cc_final: 0.7655 (ttpp) REVERT: B 188 ASP cc_start: 0.8360 (t0) cc_final: 0.8038 (t0) REVERT: B 224 GLU cc_start: 0.7512 (pp20) cc_final: 0.7195 (pp20) REVERT: C 121 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7404 (mt-10) REVERT: C 188 ASP cc_start: 0.8145 (p0) cc_final: 0.7812 (p0) REVERT: C 197 LYS cc_start: 0.6472 (mtpt) cc_final: 0.6253 (mtmt) REVERT: C 303 GLU cc_start: 0.7384 (pm20) cc_final: 0.6468 (tp30) REVERT: C 429 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6834 (tp30) REVERT: C 467 ARG cc_start: 0.7430 (mpt-90) cc_final: 0.6863 (mpt-90) REVERT: C 535 GLU cc_start: 0.8096 (mp0) cc_final: 0.7890 (mp0) REVERT: C 584 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7081 (ptp-110) REVERT: C 697 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: C 758 ASP cc_start: 0.8556 (p0) cc_final: 0.8267 (p0) REVERT: C 760 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8216 (mtp180) REVERT: C 843 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 885 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8818 (mt) REVERT: C 947 ASP cc_start: 0.7515 (p0) cc_final: 0.7142 (p0) REVERT: C 982 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: C 1051 MET cc_start: 0.8511 (ttm) cc_final: 0.8284 (mtp) REVERT: D 39 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7564 (mp) REVERT: D 123 LYS cc_start: 0.8267 (mptp) cc_final: 0.7738 (mmtm) REVERT: D 177 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.3636 (mm) REVERT: D 236 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6714 (m) REVERT: D 250 GLU cc_start: 0.7268 (tp30) cc_final: 0.6953 (mm-30) REVERT: D 285 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5952 (ptpp) REVERT: D 356 ARG cc_start: 0.7675 (ttt90) cc_final: 0.6727 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7694 (p) REVERT: D 1112 MET cc_start: 0.8017 (mmm) cc_final: 0.7622 (mtp) REVERT: D 1117 ASP cc_start: 0.7893 (p0) cc_final: 0.7598 (p0) REVERT: D 1265 ASN cc_start: 0.8312 (m-40) cc_final: 0.7868 (m-40) REVERT: E 66 ASP cc_start: 0.7817 (m-30) cc_final: 0.7225 (m-30) outliers start: 83 outliers final: 45 residues processed: 339 average time/residue: 0.6877 time to fit residues: 267.0102 Evaluate side-chains 323 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 130 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain C residue 760 ARG Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 64 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 309 optimal weight: 30.0000 chunk 218 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 chunk 260 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C1066 GLN D 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119118 restraints weight = 26287.416| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.71 r_work: 0.3133 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26486 Z= 0.123 Angle : 0.558 14.729 36360 Z= 0.294 Chirality : 0.042 0.167 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.720 178.064 4664 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 2.35 % Allowed : 19.14 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 3032 helix: 1.36 (0.16), residues: 1088 sheet: 0.04 (0.26), residues: 427 loop : -0.97 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.014 0.001 TYR A 168 PHE 0.028 0.001 PHE D 70 TRP 0.014 0.001 TRP D 723 HIS 0.002 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00277 (26478) covalent geometry : angle 0.55628 (36348) hydrogen bonds : bond 0.04511 ( 1087) hydrogen bonds : angle 4.26211 ( 3007) metal coordination : bond 0.00326 ( 8) metal coordination : angle 2.30550 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8132 (pp20) cc_final: 0.7775 (pp20) REVERT: B 55 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6394 (ptp90) REVERT: B 190 ASP cc_start: 0.8854 (m-30) cc_final: 0.8476 (m-30) REVERT: B 224 GLU cc_start: 0.7387 (pp20) cc_final: 0.7055 (pp20) REVERT: C 121 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7339 (mt-10) REVERT: C 188 ASP cc_start: 0.7918 (p0) cc_final: 0.7648 (p0) REVERT: C 257 ILE cc_start: 0.7480 (mt) cc_final: 0.7234 (mm) REVERT: C 303 GLU cc_start: 0.7244 (pm20) cc_final: 0.6336 (tp30) REVERT: C 354 THR cc_start: 0.8766 (p) cc_final: 0.8542 (t) REVERT: C 429 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6706 (tp30) REVERT: C 467 ARG cc_start: 0.7204 (mpt-90) cc_final: 0.6687 (mpt-90) REVERT: C 535 GLU cc_start: 0.7894 (mp0) cc_final: 0.7621 (mp0) REVERT: C 584 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6765 (ptp-110) REVERT: C 645 GLU cc_start: 0.8264 (tt0) cc_final: 0.7941 (mt-10) REVERT: C 758 ASP cc_start: 0.8422 (p0) cc_final: 0.8068 (p0) REVERT: C 843 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7515 (mt-10) REVERT: C 885 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8787 (mt) REVERT: C 947 ASP cc_start: 0.7528 (p0) cc_final: 0.7124 (p0) REVERT: C 1051 MET cc_start: 0.8539 (ttm) cc_final: 0.8304 (mtp) REVERT: C 1066 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8776 (mm110) REVERT: D 35 ASN cc_start: 0.7861 (t0) cc_final: 0.7374 (t0) REVERT: D 39 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7675 (mp) REVERT: D 123 LYS cc_start: 0.8123 (mptp) cc_final: 0.7594 (mmtm) REVERT: D 177 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.3669 (mm) REVERT: D 215 GLU cc_start: 0.6191 (mp0) cc_final: 0.5927 (mp0) REVERT: D 236 VAL cc_start: 0.6868 (OUTLIER) cc_final: 0.6545 (m) REVERT: D 239 ASN cc_start: 0.7757 (m-40) cc_final: 0.7531 (m110) REVERT: D 243 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7595 (mt-10) REVERT: D 250 GLU cc_start: 0.7071 (tp30) cc_final: 0.6669 (mm-30) REVERT: D 339 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7293 (t0) REVERT: D 356 ARG cc_start: 0.7683 (ttt90) cc_final: 0.6755 (ttp-110) REVERT: D 1076 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (p) REVERT: D 1087 ARG cc_start: 0.6953 (mmm-85) cc_final: 0.6644 (mtp85) REVERT: D 1112 MET cc_start: 0.7883 (mmm) cc_final: 0.7520 (mtp) REVERT: D 1117 ASP cc_start: 0.7723 (p0) cc_final: 0.7408 (p0) REVERT: D 1137 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: D 1265 ASN cc_start: 0.8220 (m-40) cc_final: 0.7777 (m-40) outliers start: 60 outliers final: 41 residues processed: 318 average time/residue: 0.6848 time to fit residues: 250.8442 Evaluate side-chains 320 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 74 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1066 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1137 GLU Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 305 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 287 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 GLN B 200 ASN C 232 GLN C 603 ASN C1066 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120556 restraints weight = 26252.668| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.77 r_work: 0.3131 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26486 Z= 0.121 Angle : 0.549 14.457 36360 Z= 0.289 Chirality : 0.042 0.170 4172 Planarity : 0.004 0.048 4401 Dihedral : 16.656 177.369 4664 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 2.35 % Allowed : 19.07 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3032 helix: 1.45 (0.16), residues: 1094 sheet: 0.07 (0.26), residues: 427 loop : -0.93 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1067 TYR 0.024 0.001 TYR D 248 PHE 0.028 0.001 PHE D 70 TRP 0.011 0.001 TRP D 723 HIS 0.002 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00274 (26478) covalent geometry : angle 0.54755 (36348) hydrogen bonds : bond 0.04366 ( 1087) hydrogen bonds : angle 4.18120 ( 3007) metal coordination : bond 0.00327 ( 8) metal coordination : angle 2.22839 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9048.51 seconds wall clock time: 154 minutes 24.72 seconds (9264.72 seconds total)