Starting phenix.real_space_refine on Sat Feb 7 03:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7y_47695/02_2026/9e7y_47695.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.038 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 124 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 18053 2.51 5 N 5231 2.21 5 O 5903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29409 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1706 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} 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: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8620 Classifications: {'peptide': 1113} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1050} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 9777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9777 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 56, 'TRANS': 1194} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 75} Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2422 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 765 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "N" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1174 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "R" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 1} Link IDs: {'rna3p': 6} Chain: "T" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1176 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12528 SG CYS D 60 78.467 69.511 58.444 1.00193.92 S ATOM 12546 SG CYS D 62 76.826 69.121 55.212 1.00207.06 S ATOM 12655 SG CYS D 75 80.521 69.393 55.407 1.00197.42 S ATOM 12681 SG CYS D 78 78.372 72.441 56.131 1.00190.49 S ATOM 19002 SG CYS D 891 109.856 108.146 104.721 1.00152.04 S ATOM 19569 SG CYS D 968 106.450 108.567 103.003 1.00143.77 S ATOM 19611 SG CYS D 975 106.942 106.057 106.130 1.00142.51 S ATOM 19629 SG CYS D 978 107.194 109.923 106.563 1.00149.14 S Time building chain proxies: 6.18, per 1000 atoms: 0.21 Number of scatterers: 29409 At special positions: 0 Unit cell: (133.424, 172.16, 187.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 95 16.00 P 124 15.00 Mg 1 11.99 O 5903 8.00 N 5231 7.00 C 18053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " Number of angles added : 12 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6398 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 47 sheets defined 43.3% alpha, 15.4% beta 54 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.580A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.590A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.114A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.721A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.030A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.543A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (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 233 through 242 removed outlier: 3.653A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.526A 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 292 through 302 removed outlier: 4.021A pdb=" N LYS C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 405 removed outlier: 4.167A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.644A 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 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.226A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 777 through 783 removed outlier: 4.073A pdb=" N ASP C 783 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.673A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.583A 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 Processing helix chain 'C' and resid 1069 through 1079 Processing helix chain 'C' and resid 1082 through 1092 Processing helix chain 'C' and resid 1097 through 1109 removed outlier: 3.533A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 4.065A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1123 " --> pdb=" O GLU C1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.623A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 142 through 187 Processing helix chain 'D' and resid 192 through 228 removed outlier: 4.031A pdb=" N ILE D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.967A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.535A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.974A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.819A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.723A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.612A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) 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 727 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.691A 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 818 removed outlier: 3.546A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.017A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 removed outlier: 3.559A pdb=" N ILE D 916 " --> pdb=" O ASP D 913 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU D 917 " --> pdb=" O PRO D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 917' Processing helix chain 'D' and resid 945 through 956 removed outlier: 3.530A pdb=" N ILE D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1144 removed outlier: 3.631A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.717A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.295A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.549A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1239 Processing helix chain 'D' and resid 1247 through 1255 removed outlier: 3.858A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1264 removed outlier: 3.817A pdb=" N ILE D1264 " --> pdb=" O GLY D1261 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.863A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.659A pdb=" N ALA E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 226 through 236 removed outlier: 3.590A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.019A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 309 removed outlier: 3.533A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 334 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.007A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.820A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.683A pdb=" N VAL F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F 479 " --> pdb=" O VAL F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 514 removed outlier: 3.873A pdb=" N ILE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 removed outlier: 3.581A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 50 through 57 removed outlier: 3.952A pdb=" N GLU M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR M 55 " --> pdb=" O GLU M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 removed outlier: 3.685A pdb=" N LEU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.590A pdb=" N ARG M 88 " --> pdb=" O ASN M 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 146 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.757A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.442A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.079A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.630A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 6.802A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.745A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.320A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.320A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.554A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.188A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.612A pdb=" N VAL C 561 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.694A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 687 " --> pdb=" O ASP C 704 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.830A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.726A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 748 through 759 removed outlier: 3.643A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 784 through 785 removed outlier: 3.682A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.710A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 906 through 907 Processing sheet with id=AD4, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.566A pdb=" N GLN D 510 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD7, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.597A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD9, first strand: chain 'D' and resid 73 through 74 removed outlier: 4.086A pdb=" N ILE D 73 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.023A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.474A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE4, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.937A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE6, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.510A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 903 through 904 removed outlier: 3.767A pdb=" N ILE D 911 " --> pdb=" O GLU D 903 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1063 through 1068 removed outlier: 3.673A pdb=" N ARG D1052 " --> pdb=" O VAL D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AF1, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AF2, first strand: chain 'J' and resid 41 through 45 1267 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.31: 4901 1.31 - 1.58: 24840 1.58 - 1.84: 408 1.84 - 2.10: 0 2.10 - 2.36: 1 Bond restraints: 30150 Sorted by residual: bond pdb=" CB PRO J 70 " pdb=" CG PRO J 70 " ideal model delta sigma weight residual 1.492 2.364 -0.872 5.00e-02 4.00e+02 3.04e+02 bond pdb=" CG PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 1.503 1.052 0.451 3.40e-02 8.65e+02 1.76e+02 bond pdb=" C1' G R 6 " pdb=" N9 G R 6 " ideal model delta sigma weight residual 1.475 1.350 0.125 1.50e-02 4.44e+03 7.00e+01 bond pdb=" N PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.40e+01 bond pdb=" C1' DG T 23 " pdb=" N9 DG T 23 " ideal model delta sigma weight residual 1.460 1.375 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 30145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.83: 41356 9.83 - 19.66: 8 19.66 - 29.49: 3 29.49 - 39.32: 0 39.32 - 49.15: 1 Bond angle restraints: 41368 Sorted by residual: angle pdb=" CB PRO J 70 " pdb=" CG PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 106.10 56.95 49.15 3.20e+00 9.77e-02 2.36e+02 angle pdb=" N PRO J 70 " pdb=" CD PRO J 70 " pdb=" CG PRO J 70 " ideal model delta sigma weight residual 103.20 88.82 14.38 1.50e+00 4.44e-01 9.19e+01 angle pdb=" O3' DC T 17 " pdb=" P DC T 18 " pdb=" OP2 DC T 18 " ideal model delta sigma weight residual 108.00 81.28 26.72 3.00e+00 1.11e-01 7.94e+01 angle pdb=" N PRO J 70 " pdb=" CA PRO J 70 " pdb=" CB PRO J 70 " ideal model delta sigma weight residual 103.25 94.70 8.55 1.05e+00 9.07e-01 6.64e+01 angle pdb=" CA PRO J 70 " pdb=" N PRO J 70 " pdb=" CD PRO J 70 " ideal model delta sigma weight residual 112.00 101.32 10.68 1.40e+00 5.10e-01 5.82e+01 ... (remaining 41363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 17128 33.70 - 67.40: 970 67.40 - 101.11: 47 101.11 - 134.81: 0 134.81 - 168.51: 2 Dihedral angle restraints: 18147 sinusoidal: 8211 harmonic: 9936 Sorted by residual: dihedral pdb=" CA ASP D1070 " pdb=" C ASP D1070 " pdb=" N GLY D1071 " pdb=" CA GLY D1071 " ideal model delta harmonic sigma weight residual -180.00 -131.03 -48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA LEU J 69 " pdb=" C LEU J 69 " pdb=" N PRO J 70 " pdb=" CA PRO J 70 " ideal model delta harmonic sigma weight residual 180.00 134.15 45.85 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA GLY D 519 " pdb=" C GLY D 519 " pdb=" N LYS D 520 " pdb=" CA LYS D 520 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 18144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 4724 0.403 - 0.807: 1 0.807 - 1.210: 0 1.210 - 1.613: 0 1.613 - 2.017: 1 Chirality restraints: 4726 Sorted by residual: chirality pdb=" P DC T 18 " pdb=" OP1 DC T 18 " pdb=" OP2 DC T 18 " pdb=" O5' DC T 18 " both_signs ideal model delta sigma weight residual True 2.35 0.33 2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" CA THR M 26 " pdb=" N THR M 26 " pdb=" C THR M 26 " pdb=" CB THR M 26 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA PRO J 70 " pdb=" N PRO J 70 " pdb=" C PRO J 70 " pdb=" CB PRO J 70 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4723 not shown) Planarity restraints: 5007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C1062 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C GLN C1062 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN C1062 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE C1063 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D1054 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ARG D1054 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG D1054 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D1055 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 300 " -0.041 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE C 300 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE C 300 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 300 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 300 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 300 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 300 " -0.028 2.00e-02 2.50e+03 ... (remaining 5004 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 303 2.54 - 3.13: 25017 3.13 - 3.72: 49272 3.72 - 4.31: 65311 4.31 - 4.90: 104997 Nonbonded interactions: 244900 Sorted by model distance: nonbonded pdb=" O PHE C 430 " pdb=" OG SER C 434 " model vdw 1.951 3.040 nonbonded pdb=" O GLY D 257 " pdb=" OG SER D 260 " model vdw 2.020 3.040 nonbonded pdb=" OD2 ASP D 539 " pdb=" O2' A R 7 " model vdw 2.039 3.040 nonbonded pdb=" OG SER D 964 " pdb=" OE1 GLU D1155 " model vdw 2.049 3.040 nonbonded pdb=" OG SER C1050 " pdb=" O THR C1053 " model vdw 2.056 3.040 ... (remaining 244895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 36.800 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.008 0.872 30158 Z= 0.308 Angle : 0.959 49.147 41380 Z= 0.502 Chirality : 0.057 2.017 4726 Planarity : 0.007 0.110 5007 Dihedral : 18.447 168.510 11749 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 0.52 % Allowed : 15.54 % Favored : 83.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3441 helix: 0.28 (0.13), residues: 1361 sheet: -0.89 (0.28), residues: 348 loop : -1.29 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 219 TYR 0.023 0.002 TYR C 306 PHE 0.051 0.003 PHE C 300 TRP 0.014 0.002 TRP M 112 HIS 0.014 0.002 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00835 (30150) covalent geometry : angle 0.95908 (41368) hydrogen bonds : bond 0.14350 ( 1389) hydrogen bonds : angle 6.64255 ( 3855) metal coordination : bond 0.09763 ( 8) metal coordination : angle 0.07024 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1337 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.7821 (p0) cc_final: 0.7475 (p0) REVERT: A 96 TYR cc_start: 0.8394 (m-80) cc_final: 0.7702 (m-10) REVERT: A 213 LYS cc_start: 0.8683 (tttt) cc_final: 0.8384 (tmtt) REVERT: A 219 PHE cc_start: 0.7716 (m-80) cc_final: 0.7415 (m-80) REVERT: B 39 ARG cc_start: 0.9160 (tmm-80) cc_final: 0.8719 (ttp-110) REVERT: B 42 LEU cc_start: 0.9613 (mt) cc_final: 0.9270 (mt) REVERT: B 120 ASN cc_start: 0.9058 (t0) cc_final: 0.8558 (t0) REVERT: B 125 ILE cc_start: 0.9359 (tp) cc_final: 0.9053 (tp) REVERT: B 151 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8666 (tm-30) REVERT: C 57 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 69 ARG cc_start: 0.8826 (ttp-170) cc_final: 0.7912 (ttt-90) REVERT: C 88 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 175 VAL cc_start: 0.9339 (t) cc_final: 0.9124 (p) REVERT: C 177 SER cc_start: 0.8758 (m) cc_final: 0.8451 (p) REVERT: C 235 THR cc_start: 0.8713 (p) cc_final: 0.8394 (p) REVERT: C 239 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7743 (mmtm) REVERT: C 277 ILE cc_start: 0.9463 (pt) cc_final: 0.9231 (pt) REVERT: C 278 TYR cc_start: 0.8710 (t80) cc_final: 0.8293 (t80) REVERT: C 319 LYS cc_start: 0.8423 (tptm) cc_final: 0.8039 (tttp) REVERT: C 404 MET cc_start: 0.8531 (mmm) cc_final: 0.8327 (tpp) REVERT: C 487 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8322 (tp30) REVERT: C 511 PHE cc_start: 0.8143 (m-80) cc_final: 0.7684 (m-10) REVERT: C 516 TYR cc_start: 0.7949 (m-80) cc_final: 0.7109 (m-80) REVERT: C 531 LEU cc_start: 0.8660 (mt) cc_final: 0.7840 (mt) REVERT: C 536 GLU cc_start: 0.8182 (tt0) cc_final: 0.7882 (tt0) REVERT: C 543 GLN cc_start: 0.7836 (tt0) cc_final: 0.7311 (mm-40) REVERT: C 578 TYR cc_start: 0.8161 (m-80) cc_final: 0.7883 (m-80) REVERT: C 586 MET cc_start: 0.8531 (ptm) cc_final: 0.8215 (ptm) REVERT: C 661 MET cc_start: 0.8264 (tpp) cc_final: 0.7786 (tpp) REVERT: C 750 ILE cc_start: 0.9249 (mm) cc_final: 0.8960 (mt) REVERT: C 820 LEU cc_start: 0.9423 (tp) cc_final: 0.9185 (tt) REVERT: C 846 LYS cc_start: 0.8904 (tptt) cc_final: 0.8637 (tppt) REVERT: C 867 GLU cc_start: 0.8535 (tt0) cc_final: 0.7836 (tp30) REVERT: C 873 VAL cc_start: 0.8851 (t) cc_final: 0.8588 (p) REVERT: C 884 LYS cc_start: 0.8099 (tttt) cc_final: 0.7652 (tttt) REVERT: C 926 MET cc_start: 0.8649 (tpt) cc_final: 0.8345 (tpp) REVERT: C 933 GLU cc_start: 0.8305 (tt0) cc_final: 0.7993 (tt0) REVERT: C 942 SER cc_start: 0.9018 (m) cc_final: 0.8568 (t) REVERT: C 947 ASP cc_start: 0.8134 (m-30) cc_final: 0.7475 (t0) REVERT: C 1024 THR cc_start: 0.9539 (m) cc_final: 0.9322 (p) REVERT: C 1040 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8339 (mptt) REVERT: C 1057 LEU cc_start: 0.9227 (tp) cc_final: 0.9021 (tp) REVERT: C 1070 GLU cc_start: 0.7812 (pm20) cc_final: 0.7110 (pm20) REVERT: C 1071 MET cc_start: 0.7824 (mpp) cc_final: 0.7311 (mpp) REVERT: C 1090 THR cc_start: 0.8890 (m) cc_final: 0.8613 (p) REVERT: C 1126 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9021 (mmtm) REVERT: C 1131 LEU cc_start: 0.9273 (mt) cc_final: 0.8962 (tt) REVERT: D 106 TYR cc_start: 0.8538 (m-80) cc_final: 0.7940 (m-80) REVERT: D 148 LEU cc_start: 0.9710 (tt) cc_final: 0.9411 (tp) REVERT: D 234 LEU cc_start: 0.8339 (pt) cc_final: 0.7595 (tp) REVERT: D 240 LEU cc_start: 0.9664 (mm) cc_final: 0.9446 (pp) REVERT: D 252 PHE cc_start: 0.7234 (p90) cc_final: 0.6961 (p90) REVERT: D 262 GLN cc_start: 0.9429 (tt0) cc_final: 0.9145 (tm-30) REVERT: D 399 LEU cc_start: 0.8833 (mm) cc_final: 0.8590 (mm) REVERT: D 427 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: D 471 SER cc_start: 0.9104 (t) cc_final: 0.7728 (t) REVERT: D 576 MET cc_start: 0.8030 (ppp) cc_final: 0.7590 (ppp) REVERT: D 581 MET cc_start: 0.8095 (mtm) cc_final: 0.7678 (mtm) REVERT: D 715 LYS cc_start: 0.9668 (mttt) cc_final: 0.9243 (mtpp) REVERT: D 765 LEU cc_start: 0.7093 (pt) cc_final: 0.6740 (mp) REVERT: D 800 ILE cc_start: 0.8717 (tp) cc_final: 0.7974 (tp) REVERT: D 838 SER cc_start: 0.6341 (m) cc_final: 0.6092 (p) REVERT: D 1139 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7322 (tm-30) REVERT: D 1235 ASP cc_start: 0.8877 (t0) cc_final: 0.8661 (m-30) REVERT: D 1238 ILE cc_start: 0.9298 (mt) cc_final: 0.9052 (mm) REVERT: D 1264 ILE cc_start: 0.8631 (pt) cc_final: 0.8363 (pt) REVERT: D 1267 TYR cc_start: 0.7853 (m-80) cc_final: 0.7179 (m-10) REVERT: E 65 ASN cc_start: 0.8828 (t0) cc_final: 0.8497 (t0) REVERT: E 66 ASP cc_start: 0.8337 (m-30) cc_final: 0.8047 (m-30) REVERT: E 67 TYR cc_start: 0.9151 (t80) cc_final: 0.8730 (t80) REVERT: E 84 GLU cc_start: 0.7975 (tp30) cc_final: 0.7681 (tp30) REVERT: E 103 LEU cc_start: 0.9169 (mt) cc_final: 0.8768 (mt) REVERT: F 263 MET cc_start: 0.8609 (mmp) cc_final: 0.8294 (mmm) REVERT: F 310 TYR cc_start: 0.7813 (m-80) cc_final: 0.7457 (m-10) REVERT: F 337 TYR cc_start: 0.7895 (p90) cc_final: 0.7469 (p90) REVERT: F 371 HIS cc_start: 0.9136 (p90) cc_final: 0.8647 (p90) REVERT: F 397 GLU cc_start: 0.9582 (pt0) cc_final: 0.9366 (pp20) REVERT: F 399 LEU cc_start: 0.9532 (mt) cc_final: 0.9223 (mm) REVERT: F 423 LEU cc_start: 0.7717 (mp) cc_final: 0.6532 (mm) REVERT: M 71 PHE cc_start: 0.9058 (m-80) cc_final: 0.8748 (m-80) outliers start: 15 outliers final: 8 residues processed: 1345 average time/residue: 0.2105 time to fit residues: 427.9762 Evaluate side-chains 931 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 923 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS C 479 HIS ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 HIS C1055 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 657 GLN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 GLN D1145 GLN ** D1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 100 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.111036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080153 restraints weight = 97848.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081468 restraints weight = 62125.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083078 restraints weight = 37198.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083648 restraints weight = 29760.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084211 restraints weight = 25056.219| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30158 Z= 0.216 Angle : 0.779 25.447 41380 Z= 0.407 Chirality : 0.054 1.922 4726 Planarity : 0.008 0.339 5007 Dihedral : 17.318 178.419 5172 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3441 helix: 0.42 (0.13), residues: 1411 sheet: -0.70 (0.26), residues: 387 loop : -1.29 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 562 TYR 0.043 0.002 TYR E 56 PHE 0.024 0.002 PHE C 300 TRP 0.023 0.003 TRP F 349 HIS 0.012 0.002 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00467 (30150) covalent geometry : angle 0.77552 (41368) hydrogen bonds : bond 0.05049 ( 1389) hydrogen bonds : angle 5.55840 ( 3855) metal coordination : bond 0.01373 ( 8) metal coordination : angle 4.35130 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1090 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8612 (tt0) cc_final: 0.8197 (tt0) REVERT: A 34 LEU cc_start: 0.9383 (tp) cc_final: 0.8932 (tp) REVERT: A 38 LEU cc_start: 0.9793 (mt) cc_final: 0.9551 (mt) REVERT: A 90 ASP cc_start: 0.8927 (p0) cc_final: 0.8476 (p0) REVERT: A 138 LEU cc_start: 0.9368 (mp) cc_final: 0.8957 (mp) REVERT: A 140 VAL cc_start: 0.9522 (t) cc_final: 0.8781 (m) REVERT: A 141 GLU cc_start: 0.8273 (tp30) cc_final: 0.7598 (mm-30) REVERT: A 165 ASP cc_start: 0.8902 (m-30) cc_final: 0.8630 (m-30) REVERT: A 179 ASP cc_start: 0.7844 (p0) cc_final: 0.7642 (p0) REVERT: A 208 LEU cc_start: 0.9550 (mm) cc_final: 0.9342 (mt) REVERT: B 20 GLN cc_start: 0.8849 (mp10) cc_final: 0.8276 (mp10) REVERT: B 95 MET cc_start: 0.8221 (ttt) cc_final: 0.7924 (ttt) REVERT: B 120 ASN cc_start: 0.9362 (t0) cc_final: 0.8889 (t0) REVERT: B 151 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8605 (tm-30) REVERT: B 188 ASP cc_start: 0.9535 (t70) cc_final: 0.9319 (t0) REVERT: B 197 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8868 (tp30) REVERT: B 213 LYS cc_start: 0.9535 (tptp) cc_final: 0.9305 (tppt) REVERT: B 215 LEU cc_start: 0.9336 (mm) cc_final: 0.9117 (mm) REVERT: B 216 VAL cc_start: 0.8915 (t) cc_final: 0.8709 (t) REVERT: B 219 PHE cc_start: 0.8984 (m-80) cc_final: 0.8778 (m-80) REVERT: B 223 ARG cc_start: 0.9158 (ttt-90) cc_final: 0.8893 (tpt-90) REVERT: C 57 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9017 (mm-40) REVERT: C 59 ASP cc_start: 0.9552 (m-30) cc_final: 0.9331 (m-30) REVERT: C 87 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8778 (mp0) REVERT: C 90 LEU cc_start: 0.9725 (mt) cc_final: 0.9498 (pp) REVERT: C 93 LEU cc_start: 0.9281 (tp) cc_final: 0.8974 (tp) REVERT: C 102 SER cc_start: 0.8851 (m) cc_final: 0.8297 (p) REVERT: C 127 MET cc_start: 0.8939 (tmm) cc_final: 0.8046 (tmm) REVERT: C 173 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8196 (mmm160) REVERT: C 177 SER cc_start: 0.9068 (m) cc_final: 0.8748 (t) REVERT: C 199 LEU cc_start: 0.9349 (pp) cc_final: 0.8937 (mt) REVERT: C 202 VAL cc_start: 0.9368 (p) cc_final: 0.9100 (p) REVERT: C 252 PHE cc_start: 0.8975 (m-80) cc_final: 0.8571 (m-80) REVERT: C 265 ASP cc_start: 0.8196 (t0) cc_final: 0.7917 (t0) REVERT: C 393 MET cc_start: 0.9582 (mmm) cc_final: 0.9318 (mmm) REVERT: C 420 ILE cc_start: 0.9220 (mm) cc_final: 0.8942 (tp) REVERT: C 438 GLN cc_start: 0.8549 (mt0) cc_final: 0.8161 (mt0) REVERT: C 442 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8220 (tp-100) REVERT: C 511 PHE cc_start: 0.8706 (m-80) cc_final: 0.7979 (m-10) REVERT: C 516 TYR cc_start: 0.8483 (m-80) cc_final: 0.7558 (m-80) REVERT: C 531 LEU cc_start: 0.8618 (mt) cc_final: 0.8244 (mp) REVERT: C 536 GLU cc_start: 0.8832 (pt0) cc_final: 0.8509 (pt0) REVERT: C 543 GLN cc_start: 0.8300 (tt0) cc_final: 0.7416 (pp30) REVERT: C 585 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8124 (tp-100) REVERT: C 586 MET cc_start: 0.9088 (ptm) cc_final: 0.8769 (ptp) REVERT: C 601 ASP cc_start: 0.9261 (t0) cc_final: 0.8668 (p0) REVERT: C 620 ARG cc_start: 0.9321 (tpm170) cc_final: 0.8957 (tpm170) REVERT: C 630 MET cc_start: 0.8740 (mmp) cc_final: 0.8492 (mmp) REVERT: C 675 PHE cc_start: 0.9203 (m-10) cc_final: 0.8976 (m-10) REVERT: C 749 SER cc_start: 0.9583 (m) cc_final: 0.8997 (p) REVERT: C 773 ILE cc_start: 0.7214 (mm) cc_final: 0.6689 (mm) REVERT: C 839 VAL cc_start: 0.9099 (t) cc_final: 0.8731 (t) REVERT: C 846 LYS cc_start: 0.9265 (tptt) cc_final: 0.8907 (tppt) REVERT: C 850 ILE cc_start: 0.8668 (mp) cc_final: 0.8417 (mm) REVERT: C 873 VAL cc_start: 0.9186 (t) cc_final: 0.8715 (p) REVERT: C 889 HIS cc_start: 0.8592 (m-70) cc_final: 0.8258 (m-70) REVERT: C 892 LYS cc_start: 0.9163 (ptpt) cc_final: 0.8742 (ptpt) REVERT: C 926 MET cc_start: 0.8881 (tpt) cc_final: 0.8582 (tpp) REVERT: C 933 GLU cc_start: 0.8594 (tt0) cc_final: 0.8179 (tt0) REVERT: C 939 CYS cc_start: 0.9330 (m) cc_final: 0.9076 (m) REVERT: C 942 SER cc_start: 0.8941 (m) cc_final: 0.8689 (t) REVERT: C 944 TRP cc_start: 0.8765 (p90) cc_final: 0.8170 (p90) REVERT: C 947 ASP cc_start: 0.9098 (m-30) cc_final: 0.8141 (t0) REVERT: C 985 LEU cc_start: 0.9564 (mm) cc_final: 0.9318 (mm) REVERT: C 1031 MET cc_start: 0.8792 (mtm) cc_final: 0.8093 (mtm) REVERT: C 1039 ASP cc_start: 0.9194 (m-30) cc_final: 0.8964 (m-30) REVERT: C 1040 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7914 (mptt) REVERT: C 1071 MET cc_start: 0.8325 (mpp) cc_final: 0.7324 (pmm) REVERT: C 1076 MET cc_start: 0.8941 (ttm) cc_final: 0.8608 (ttm) REVERT: C 1090 THR cc_start: 0.8947 (m) cc_final: 0.8722 (p) REVERT: C 1128 LEU cc_start: 0.9670 (mt) cc_final: 0.9237 (mt) REVERT: C 1133 LEU cc_start: 0.9401 (mt) cc_final: 0.9034 (mt) REVERT: D 12 ILE cc_start: 0.9071 (tt) cc_final: 0.8809 (pt) REVERT: D 29 LYS cc_start: 0.9264 (ptpp) cc_final: 0.8904 (ptpp) REVERT: D 33 THR cc_start: 0.8689 (p) cc_final: 0.8366 (p) REVERT: D 52 PHE cc_start: 0.7853 (m-80) cc_final: 0.7006 (m-10) REVERT: D 92 MET cc_start: 0.7719 (mmm) cc_final: 0.7288 (tpt) REVERT: D 113 ARG cc_start: 0.9365 (mpt180) cc_final: 0.9113 (mmt90) REVERT: D 118 LEU cc_start: 0.9338 (mm) cc_final: 0.8917 (mm) REVERT: D 119 ASP cc_start: 0.8521 (t70) cc_final: 0.8039 (t0) REVERT: D 120 LEU cc_start: 0.8935 (mm) cc_final: 0.8394 (tp) REVERT: D 127 LYS cc_start: 0.9774 (mtmm) cc_final: 0.9544 (ptpp) REVERT: D 205 MET cc_start: 0.8901 (mmm) cc_final: 0.8550 (mmm) REVERT: D 252 PHE cc_start: 0.8219 (p90) cc_final: 0.7843 (p90) REVERT: D 262 GLN cc_start: 0.9657 (tt0) cc_final: 0.9089 (tm-30) REVERT: D 341 ASN cc_start: 0.8943 (m-40) cc_final: 0.8664 (m-40) REVERT: D 346 ARG cc_start: 0.9140 (ttm110) cc_final: 0.8198 (ptp-110) REVERT: D 382 PHE cc_start: 0.9062 (m-80) cc_final: 0.8760 (m-80) REVERT: D 397 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.8413 (tmm-80) REVERT: D 427 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: D 471 SER cc_start: 0.9377 (t) cc_final: 0.9098 (p) REVERT: D 475 MET cc_start: 0.9014 (mmp) cc_final: 0.8704 (mmp) REVERT: D 503 THR cc_start: 0.8952 (p) cc_final: 0.7836 (p) REVERT: D 504 LEU cc_start: 0.9218 (tp) cc_final: 0.8922 (tp) REVERT: D 515 MET cc_start: 0.8434 (mmp) cc_final: 0.8069 (mmm) REVERT: D 527 LEU cc_start: 0.9416 (mt) cc_final: 0.9194 (mt) REVERT: D 563 ASN cc_start: 0.8970 (m-40) cc_final: 0.8690 (m-40) REVERT: D 581 MET cc_start: 0.8787 (mtm) cc_final: 0.8169 (mtm) REVERT: D 675 GLU cc_start: 0.9291 (tm-30) cc_final: 0.9013 (tm-30) REVERT: D 706 MET cc_start: 0.8641 (ptm) cc_final: 0.8408 (pmm) REVERT: D 707 ILE cc_start: 0.9451 (tt) cc_final: 0.9212 (tt) REVERT: D 715 LYS cc_start: 0.9710 (mttt) cc_final: 0.9373 (mtpt) REVERT: D 757 GLU cc_start: 0.9236 (tm-30) cc_final: 0.9015 (tm-30) REVERT: D 780 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8829 (mm-30) REVERT: D 784 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9067 (mm-30) REVERT: D 800 ILE cc_start: 0.9387 (tp) cc_final: 0.9067 (tp) REVERT: D 804 ASP cc_start: 0.8702 (m-30) cc_final: 0.8446 (p0) REVERT: D 840 PHE cc_start: 0.8787 (m-80) cc_final: 0.8577 (m-80) REVERT: D 844 LEU cc_start: 0.8714 (mm) cc_final: 0.7770 (tp) REVERT: D 862 ASP cc_start: 0.9032 (t0) cc_final: 0.8708 (t0) REVERT: D 866 ARG cc_start: 0.9192 (ptt180) cc_final: 0.8569 (ptt-90) REVERT: D 928 ASP cc_start: 0.8460 (m-30) cc_final: 0.8066 (m-30) REVERT: D 990 ASP cc_start: 0.8325 (m-30) cc_final: 0.7909 (m-30) REVERT: D 1032 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9027 (tm-30) REVERT: D 1036 GLU cc_start: 0.8503 (tp30) cc_final: 0.7587 (tt0) REVERT: D 1133 HIS cc_start: 0.9173 (t70) cc_final: 0.8856 (t70) REVERT: D 1137 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9151 (mm-30) REVERT: D 1183 ARG cc_start: 0.9307 (ptp-110) cc_final: 0.9053 (ptp-110) REVERT: D 1208 MET cc_start: 0.8533 (mpp) cc_final: 0.8268 (mpp) REVERT: D 1229 THR cc_start: 0.9466 (m) cc_final: 0.9198 (m) REVERT: E 65 ASN cc_start: 0.9081 (t0) cc_final: 0.8877 (t0) REVERT: E 66 ASP cc_start: 0.8715 (m-30) cc_final: 0.8340 (m-30) REVERT: E 79 VAL cc_start: 0.9058 (t) cc_final: 0.8575 (m) REVERT: E 103 LEU cc_start: 0.9185 (mt) cc_final: 0.8925 (mt) REVERT: F 251 LYS cc_start: 0.9254 (mttm) cc_final: 0.8972 (mtmm) REVERT: F 252 ARG cc_start: 0.9206 (mtp85) cc_final: 0.8668 (mmm160) REVERT: F 263 MET cc_start: 0.8706 (mmp) cc_final: 0.8493 (mmm) REVERT: F 333 GLU cc_start: 0.8429 (tt0) cc_final: 0.7487 (tm-30) REVERT: F 334 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7802 (mmmt) REVERT: F 339 LYS cc_start: 0.9245 (ptpt) cc_final: 0.8729 (ptpp) REVERT: F 372 MET cc_start: 0.9601 (mmp) cc_final: 0.9310 (mmm) REVERT: F 412 GLU cc_start: 0.9688 (tp30) cc_final: 0.9300 (tp30) REVERT: F 415 GLN cc_start: 0.9734 (tm-30) cc_final: 0.9471 (tm-30) REVERT: F 482 THR cc_start: 0.8687 (m) cc_final: 0.8451 (p) REVERT: F 525 ASP cc_start: 0.9199 (m-30) cc_final: 0.8605 (p0) REVERT: J 32 TYR cc_start: 0.8629 (m-80) cc_final: 0.8193 (m-80) REVERT: J 84 MET cc_start: 0.9478 (mpp) cc_final: 0.8983 (mpp) REVERT: J 86 LEU cc_start: 0.9638 (tp) cc_final: 0.9332 (mt) REVERT: M 87 ARG cc_start: 0.9521 (tpt-90) cc_final: 0.9230 (tpp-160) REVERT: M 156 GLU cc_start: 0.9688 (tm-30) cc_final: 0.9399 (mm-30) outliers start: 9 outliers final: 2 residues processed: 1095 average time/residue: 0.2168 time to fit residues: 362.6958 Evaluate side-chains 852 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 850 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 36 ASN C 232 GLN C 323 HIS ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS C 729 HIS C 935 HIS C1055 GLN C1129 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN D 564 ASN D 674 ASN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN D1084 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN F 322 GLN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.110669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079890 restraints weight = 98763.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080824 restraints weight = 59215.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082486 restraints weight = 35767.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082957 restraints weight = 28076.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083423 restraints weight = 25264.989| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30158 Z= 0.178 Angle : 0.734 25.362 41380 Z= 0.381 Chirality : 0.053 1.944 4726 Planarity : 0.007 0.339 5007 Dihedral : 17.338 178.873 5172 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3441 helix: 0.46 (0.13), residues: 1405 sheet: -0.66 (0.26), residues: 368 loop : -1.16 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 562 TYR 0.028 0.002 TYR E 56 PHE 0.026 0.002 PHE C 300 TRP 0.043 0.002 TRP M 112 HIS 0.013 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00383 (30150) covalent geometry : angle 0.73198 (41368) hydrogen bonds : bond 0.04541 ( 1389) hydrogen bonds : angle 5.27137 ( 3855) metal coordination : bond 0.00923 ( 8) metal coordination : angle 3.12852 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1030 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8456 (tt0) cc_final: 0.7909 (tt0) REVERT: A 34 LEU cc_start: 0.9416 (tp) cc_final: 0.9027 (tp) REVERT: A 78 LEU cc_start: 0.9572 (tp) cc_final: 0.9334 (tp) REVERT: A 138 LEU cc_start: 0.9411 (mp) cc_final: 0.9031 (mp) REVERT: A 165 ASP cc_start: 0.8937 (m-30) cc_final: 0.8587 (m-30) REVERT: A 208 LEU cc_start: 0.9596 (mm) cc_final: 0.9348 (mm) REVERT: A 215 LEU cc_start: 0.9655 (mt) cc_final: 0.9348 (mm) REVERT: A 219 PHE cc_start: 0.8004 (m-80) cc_final: 0.7525 (m-80) REVERT: B 14 LEU cc_start: 0.9346 (mt) cc_final: 0.9121 (mt) REVERT: B 18 ARG cc_start: 0.9209 (ttp-110) cc_final: 0.8850 (ttp-110) REVERT: B 20 GLN cc_start: 0.8839 (mp10) cc_final: 0.8049 (mp10) REVERT: B 39 ARG cc_start: 0.9293 (tmm-80) cc_final: 0.8793 (ttm170) REVERT: B 42 LEU cc_start: 0.9801 (mt) cc_final: 0.9572 (mt) REVERT: B 44 SER cc_start: 0.9217 (m) cc_final: 0.8280 (t) REVERT: B 120 ASN cc_start: 0.9390 (t0) cc_final: 0.8914 (t0) REVERT: B 151 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8606 (tm-30) REVERT: B 165 ASP cc_start: 0.8961 (m-30) cc_final: 0.8246 (m-30) REVERT: B 188 ASP cc_start: 0.9551 (t70) cc_final: 0.9317 (t0) REVERT: B 213 LYS cc_start: 0.9582 (tptp) cc_final: 0.9355 (tppt) REVERT: B 217 GLU cc_start: 0.9508 (pt0) cc_final: 0.9202 (tm-30) REVERT: B 219 PHE cc_start: 0.9062 (m-80) cc_final: 0.8408 (m-80) REVERT: C 48 LEU cc_start: 0.9010 (mm) cc_final: 0.8801 (mm) REVERT: C 57 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8930 (mm-40) REVERT: C 87 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8738 (mp0) REVERT: C 91 TYR cc_start: 0.9291 (t80) cc_final: 0.9075 (t80) REVERT: C 102 SER cc_start: 0.8753 (m) cc_final: 0.8199 (p) REVERT: C 127 MET cc_start: 0.8720 (tmm) cc_final: 0.8263 (tmm) REVERT: C 177 SER cc_start: 0.9038 (m) cc_final: 0.8753 (t) REVERT: C 199 LEU cc_start: 0.9295 (pp) cc_final: 0.8948 (mt) REVERT: C 213 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7162 (mm-30) REVERT: C 239 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7847 (tppt) REVERT: C 263 GLU cc_start: 0.8824 (mp0) cc_final: 0.8590 (mp0) REVERT: C 264 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8868 (ptpp) REVERT: C 308 LEU cc_start: 0.9467 (mm) cc_final: 0.9182 (mm) REVERT: C 420 ILE cc_start: 0.9205 (mm) cc_final: 0.8936 (tp) REVERT: C 442 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8485 (tp-100) REVERT: C 466 GLU cc_start: 0.9304 (pm20) cc_final: 0.9023 (pm20) REVERT: C 511 PHE cc_start: 0.8836 (m-80) cc_final: 0.8023 (m-10) REVERT: C 516 TYR cc_start: 0.8533 (m-80) cc_final: 0.7901 (m-80) REVERT: C 531 LEU cc_start: 0.8530 (mt) cc_final: 0.8009 (mt) REVERT: C 543 GLN cc_start: 0.8300 (tt0) cc_final: 0.6887 (mm-40) REVERT: C 560 LEU cc_start: 0.8118 (mm) cc_final: 0.7824 (mm) REVERT: C 601 ASP cc_start: 0.9292 (t0) cc_final: 0.8783 (p0) REVERT: C 630 MET cc_start: 0.8682 (mmp) cc_final: 0.8463 (mmp) REVERT: C 675 PHE cc_start: 0.9100 (m-10) cc_final: 0.8791 (m-10) REVERT: C 741 LEU cc_start: 0.9474 (mt) cc_final: 0.9191 (mt) REVERT: C 749 SER cc_start: 0.9347 (m) cc_final: 0.8871 (p) REVERT: C 753 GLU cc_start: 0.8217 (mp0) cc_final: 0.8008 (mp0) REVERT: C 839 VAL cc_start: 0.9230 (t) cc_final: 0.8908 (t) REVERT: C 846 LYS cc_start: 0.9272 (tptt) cc_final: 0.8868 (tppt) REVERT: C 873 VAL cc_start: 0.9104 (t) cc_final: 0.8398 (p) REVERT: C 892 LYS cc_start: 0.9182 (ptpt) cc_final: 0.8770 (ptpt) REVERT: C 918 ASN cc_start: 0.7324 (t0) cc_final: 0.7117 (t0) REVERT: C 926 MET cc_start: 0.8963 (tpt) cc_final: 0.8671 (tpp) REVERT: C 933 GLU cc_start: 0.8513 (tt0) cc_final: 0.8233 (tt0) REVERT: C 939 CYS cc_start: 0.9333 (m) cc_final: 0.9093 (m) REVERT: C 942 SER cc_start: 0.8895 (m) cc_final: 0.8649 (t) REVERT: C 944 TRP cc_start: 0.8788 (p90) cc_final: 0.8101 (p90) REVERT: C 963 LEU cc_start: 0.8417 (mt) cc_final: 0.8014 (mt) REVERT: C 1001 LEU cc_start: 0.9081 (mt) cc_final: 0.8710 (mp) REVERT: C 1021 TYR cc_start: 0.8268 (m-80) cc_final: 0.8023 (m-80) REVERT: C 1031 MET cc_start: 0.8896 (mtm) cc_final: 0.8335 (mtm) REVERT: C 1039 ASP cc_start: 0.9182 (m-30) cc_final: 0.8804 (m-30) REVERT: C 1040 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7797 (mptt) REVERT: C 1051 MET cc_start: 0.9117 (mmm) cc_final: 0.8909 (tpp) REVERT: C 1077 GLN cc_start: 0.9406 (mt0) cc_final: 0.9140 (mt0) REVERT: C 1090 THR cc_start: 0.9075 (m) cc_final: 0.8840 (p) REVERT: C 1127 GLU cc_start: 0.9039 (pp20) cc_final: 0.8741 (pp20) REVERT: C 1128 LEU cc_start: 0.9472 (mt) cc_final: 0.9255 (mt) REVERT: C 1138 LEU cc_start: 0.8743 (mt) cc_final: 0.8387 (tp) REVERT: D 29 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8990 (ptpp) REVERT: D 52 PHE cc_start: 0.7949 (m-80) cc_final: 0.7193 (m-10) REVERT: D 64 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8309 (mtpt) REVERT: D 66 LYS cc_start: 0.9237 (ptpp) cc_final: 0.8985 (mmmt) REVERT: D 92 MET cc_start: 0.8469 (mmm) cc_final: 0.7969 (mmm) REVERT: D 118 LEU cc_start: 0.9379 (mm) cc_final: 0.8954 (mm) REVERT: D 119 ASP cc_start: 0.8475 (t70) cc_final: 0.8134 (t0) REVERT: D 120 LEU cc_start: 0.8954 (mm) cc_final: 0.8446 (tp) REVERT: D 256 MET cc_start: 0.7615 (tpp) cc_final: 0.6996 (tpp) REVERT: D 262 GLN cc_start: 0.9598 (tt0) cc_final: 0.9082 (tm-30) REVERT: D 302 PHE cc_start: 0.9143 (m-80) cc_final: 0.8934 (m-10) REVERT: D 341 ASN cc_start: 0.8861 (m-40) cc_final: 0.8507 (m-40) REVERT: D 345 ARG cc_start: 0.8885 (ttt-90) cc_final: 0.8477 (ttt180) REVERT: D 346 ARG cc_start: 0.9232 (ttm110) cc_final: 0.8265 (ptp-110) REVERT: D 397 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.8439 (tmm-80) REVERT: D 427 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: D 471 SER cc_start: 0.9160 (t) cc_final: 0.8468 (p) REVERT: D 475 MET cc_start: 0.9003 (mmp) cc_final: 0.8731 (mmp) REVERT: D 504 LEU cc_start: 0.9281 (tp) cc_final: 0.8939 (tp) REVERT: D 505 HIS cc_start: 0.9321 (p-80) cc_final: 0.9082 (p-80) REVERT: D 509 ILE cc_start: 0.8835 (tt) cc_final: 0.8447 (tp) REVERT: D 510 GLN cc_start: 0.8006 (mp10) cc_final: 0.7615 (mp10) REVERT: D 515 MET cc_start: 0.8535 (mmp) cc_final: 0.8204 (mmm) REVERT: D 532 PHE cc_start: 0.8114 (m-10) cc_final: 0.7662 (m-80) REVERT: D 545 LEU cc_start: 0.9425 (tp) cc_final: 0.9212 (tp) REVERT: D 552 GLN cc_start: 0.8442 (mp10) cc_final: 0.8237 (mp10) REVERT: D 560 LEU cc_start: 0.9556 (tp) cc_final: 0.9354 (tp) REVERT: D 563 ASN cc_start: 0.8890 (m-40) cc_final: 0.8663 (m-40) REVERT: D 572 ARG cc_start: 0.8417 (mpp80) cc_final: 0.8140 (mpp80) REVERT: D 574 LEU cc_start: 0.9016 (mt) cc_final: 0.8812 (mt) REVERT: D 576 MET cc_start: 0.9007 (ppp) cc_final: 0.8721 (ppp) REVERT: D 581 MET cc_start: 0.8849 (mtm) cc_final: 0.8481 (mtm) REVERT: D 641 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8628 (tpp80) REVERT: D 706 MET cc_start: 0.8546 (ptm) cc_final: 0.8315 (pmm) REVERT: D 757 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8966 (tm-30) REVERT: D 779 LYS cc_start: 0.9646 (pttm) cc_final: 0.9384 (pttm) REVERT: D 780 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8849 (mm-30) REVERT: D 784 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9073 (mm-30) REVERT: D 800 ILE cc_start: 0.9360 (tp) cc_final: 0.8998 (tp) REVERT: D 840 PHE cc_start: 0.8916 (m-80) cc_final: 0.8709 (m-80) REVERT: D 844 LEU cc_start: 0.8759 (mm) cc_final: 0.7914 (tp) REVERT: D 866 ARG cc_start: 0.9244 (ptt180) cc_final: 0.8992 (ptt-90) REVERT: D 917 GLU cc_start: 0.9155 (mp0) cc_final: 0.8843 (mp0) REVERT: D 928 ASP cc_start: 0.8573 (m-30) cc_final: 0.8194 (m-30) REVERT: D 990 ASP cc_start: 0.8448 (m-30) cc_final: 0.8209 (m-30) REVERT: D 1028 LEU cc_start: 0.9580 (tt) cc_final: 0.9126 (tt) REVERT: D 1036 GLU cc_start: 0.8649 (tp30) cc_final: 0.8057 (tp30) REVERT: D 1125 GLN cc_start: 0.8971 (mt0) cc_final: 0.8715 (mp10) REVERT: D 1129 GLU cc_start: 0.9400 (mp0) cc_final: 0.9195 (mp0) REVERT: D 1133 HIS cc_start: 0.9183 (t70) cc_final: 0.8865 (t70) REVERT: D 1137 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9168 (mm-30) REVERT: D 1139 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8874 (tp-100) REVERT: D 1151 ASP cc_start: 0.8472 (t0) cc_final: 0.8090 (t0) REVERT: D 1183 ARG cc_start: 0.9310 (ptp-110) cc_final: 0.8919 (ptp-170) REVERT: D 1267 TYR cc_start: 0.8661 (m-80) cc_final: 0.8427 (m-80) REVERT: E 43 LEU cc_start: 0.9713 (mm) cc_final: 0.9470 (mm) REVERT: E 65 ASN cc_start: 0.9179 (t0) cc_final: 0.8907 (t0) REVERT: E 66 ASP cc_start: 0.8702 (m-30) cc_final: 0.8249 (m-30) REVERT: E 78 TYR cc_start: 0.8440 (m-10) cc_final: 0.8214 (m-10) REVERT: E 79 VAL cc_start: 0.9213 (t) cc_final: 0.8820 (m) REVERT: E 90 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8859 (mttt) REVERT: F 258 TYR cc_start: 0.9179 (t80) cc_final: 0.8926 (t80) REVERT: F 282 MET cc_start: 0.9208 (mpp) cc_final: 0.8927 (ptp) REVERT: F 333 GLU cc_start: 0.8525 (tt0) cc_final: 0.7552 (tm-30) REVERT: F 334 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7771 (mmmt) REVERT: F 339 LYS cc_start: 0.9192 (ptpt) cc_final: 0.8675 (ptpp) REVERT: F 359 MET cc_start: 0.9326 (tpp) cc_final: 0.9089 (mmt) REVERT: F 372 MET cc_start: 0.9573 (mmp) cc_final: 0.9280 (mmm) REVERT: F 412 GLU cc_start: 0.9697 (tp30) cc_final: 0.9210 (tp30) REVERT: F 441 ASP cc_start: 0.8484 (t0) cc_final: 0.7623 (t0) REVERT: F 485 GLN cc_start: 0.9041 (mp10) cc_final: 0.8666 (pm20) REVERT: F 490 ASP cc_start: 0.8882 (m-30) cc_final: 0.8682 (p0) REVERT: J 54 TRP cc_start: 0.8753 (t-100) cc_final: 0.8470 (t-100) REVERT: J 55 LEU cc_start: 0.9329 (tp) cc_final: 0.9044 (tp) REVERT: J 84 MET cc_start: 0.9394 (mpp) cc_final: 0.8762 (mpp) REVERT: J 86 LEU cc_start: 0.9626 (tp) cc_final: 0.9321 (mt) REVERT: M 84 ASN cc_start: 0.9153 (p0) cc_final: 0.8588 (p0) REVERT: M 112 TRP cc_start: 0.8798 (t60) cc_final: 0.8511 (t60) REVERT: M 156 GLU cc_start: 0.9714 (tm-30) cc_final: 0.9414 (mm-30) outliers start: 5 outliers final: 0 residues processed: 1031 average time/residue: 0.2054 time to fit residues: 327.3563 Evaluate side-chains 841 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 841 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 229 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 344 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS D 233 GLN D 369 ASN D 410 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.109294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078398 restraints weight = 99428.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079972 restraints weight = 58074.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081278 restraints weight = 36588.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081715 restraints weight = 28979.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082238 restraints weight = 25148.984| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30158 Z= 0.178 Angle : 0.717 25.657 41380 Z= 0.371 Chirality : 0.052 1.938 4726 Planarity : 0.007 0.306 5007 Dihedral : 17.351 179.740 5172 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 0.17 % Allowed : 3.95 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3441 helix: 0.44 (0.14), residues: 1388 sheet: -0.64 (0.26), residues: 391 loop : -1.13 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 75 TYR 0.026 0.002 TYR E 56 PHE 0.020 0.002 PHE C 300 TRP 0.034 0.002 TRP M 112 HIS 0.011 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00390 (30150) covalent geometry : angle 0.71391 (41368) hydrogen bonds : bond 0.04348 ( 1389) hydrogen bonds : angle 5.16053 ( 3855) metal coordination : bond 0.01087 ( 8) metal coordination : angle 3.68577 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 983 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8408 (tt0) cc_final: 0.7879 (tt0) REVERT: A 34 LEU cc_start: 0.9437 (tp) cc_final: 0.9055 (tp) REVERT: A 90 ASP cc_start: 0.8980 (p0) cc_final: 0.8537 (p0) REVERT: A 138 LEU cc_start: 0.9385 (mp) cc_final: 0.9025 (mp) REVERT: A 141 GLU cc_start: 0.8148 (tp30) cc_final: 0.7434 (mm-30) REVERT: A 151 GLN cc_start: 0.8234 (mp-120) cc_final: 0.7810 (pm20) REVERT: A 172 LEU cc_start: 0.9680 (mt) cc_final: 0.9436 (mt) REVERT: A 197 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 208 LEU cc_start: 0.9635 (mm) cc_final: 0.9432 (mm) REVERT: A 219 PHE cc_start: 0.8112 (m-80) cc_final: 0.7686 (m-80) REVERT: B 18 ARG cc_start: 0.9057 (ttp-110) cc_final: 0.8764 (ttp-110) REVERT: B 20 GLN cc_start: 0.8709 (mp10) cc_final: 0.7946 (mp10) REVERT: B 39 ARG cc_start: 0.9322 (tmm-80) cc_final: 0.8927 (ttm170) REVERT: B 40 ARG cc_start: 0.9144 (mmp-170) cc_final: 0.8927 (mmm160) REVERT: B 42 LEU cc_start: 0.9801 (mt) cc_final: 0.9569 (mt) REVERT: B 44 SER cc_start: 0.9247 (m) cc_final: 0.8271 (t) REVERT: B 120 ASN cc_start: 0.9402 (t0) cc_final: 0.8942 (t0) REVERT: B 151 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8615 (tm-30) REVERT: B 213 LYS cc_start: 0.9589 (tptp) cc_final: 0.9366 (tppt) REVERT: B 217 GLU cc_start: 0.9480 (pt0) cc_final: 0.9193 (tm-30) REVERT: B 219 PHE cc_start: 0.9137 (m-80) cc_final: 0.8625 (m-80) REVERT: C 59 ASP cc_start: 0.9467 (m-30) cc_final: 0.9247 (m-30) REVERT: C 87 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8753 (mp0) REVERT: C 93 LEU cc_start: 0.9441 (tp) cc_final: 0.9137 (tp) REVERT: C 127 MET cc_start: 0.8718 (tmm) cc_final: 0.8292 (tmm) REVERT: C 129 TYR cc_start: 0.8599 (t80) cc_final: 0.8369 (t80) REVERT: C 177 SER cc_start: 0.9095 (m) cc_final: 0.8842 (t) REVERT: C 199 LEU cc_start: 0.9237 (pp) cc_final: 0.8890 (mt) REVERT: C 239 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7785 (tppt) REVERT: C 264 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8887 (ptpp) REVERT: C 279 ARG cc_start: 0.9627 (tmt170) cc_final: 0.9421 (ptp-110) REVERT: C 466 GLU cc_start: 0.9254 (pm20) cc_final: 0.8954 (pm20) REVERT: C 482 ARG cc_start: 0.8941 (mtt180) cc_final: 0.7161 (mmt90) REVERT: C 511 PHE cc_start: 0.9075 (m-80) cc_final: 0.8263 (m-10) REVERT: C 516 TYR cc_start: 0.8598 (m-80) cc_final: 0.7759 (m-80) REVERT: C 531 LEU cc_start: 0.8559 (mt) cc_final: 0.8096 (mp) REVERT: C 543 GLN cc_start: 0.7838 (tt0) cc_final: 0.7430 (tm-30) REVERT: C 579 MET cc_start: 0.8995 (ppp) cc_final: 0.8219 (tmm) REVERT: C 585 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8363 (tp40) REVERT: C 601 ASP cc_start: 0.9259 (t0) cc_final: 0.8629 (p0) REVERT: C 620 ARG cc_start: 0.9276 (tpm170) cc_final: 0.8922 (tpm170) REVERT: C 846 LYS cc_start: 0.9212 (tptt) cc_final: 0.8787 (tppt) REVERT: C 873 VAL cc_start: 0.9159 (t) cc_final: 0.8749 (p) REVERT: C 892 LYS cc_start: 0.9284 (ptpt) cc_final: 0.8834 (ptpt) REVERT: C 904 MET cc_start: 0.9188 (tpp) cc_final: 0.8771 (ttm) REVERT: C 926 MET cc_start: 0.8967 (tpt) cc_final: 0.8381 (tpp) REVERT: C 939 CYS cc_start: 0.9355 (m) cc_final: 0.9133 (m) REVERT: C 944 TRP cc_start: 0.8792 (p90) cc_final: 0.8429 (p90) REVERT: C 1021 TYR cc_start: 0.8403 (m-80) cc_final: 0.8147 (m-80) REVERT: C 1031 MET cc_start: 0.8869 (mtm) cc_final: 0.8426 (mtm) REVERT: C 1039 ASP cc_start: 0.9236 (m-30) cc_final: 0.8832 (m-30) REVERT: C 1040 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7797 (mptt) REVERT: C 1076 MET cc_start: 0.8935 (ttm) cc_final: 0.8726 (ttm) REVERT: C 1077 GLN cc_start: 0.9477 (mt0) cc_final: 0.9147 (mt0) REVERT: C 1090 THR cc_start: 0.9101 (m) cc_final: 0.8856 (p) REVERT: C 1128 LEU cc_start: 0.9303 (mt) cc_final: 0.8981 (mt) REVERT: D 29 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8938 (ptpp) REVERT: D 52 PHE cc_start: 0.8020 (m-80) cc_final: 0.6730 (m-10) REVERT: D 64 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8369 (mtpt) REVERT: D 66 LYS cc_start: 0.9242 (ptpp) cc_final: 0.9005 (mmmt) REVERT: D 92 MET cc_start: 0.8437 (mmm) cc_final: 0.8176 (mmm) REVERT: D 118 LEU cc_start: 0.9392 (mm) cc_final: 0.8944 (mm) REVERT: D 119 ASP cc_start: 0.8487 (t70) cc_final: 0.8137 (t0) REVERT: D 120 LEU cc_start: 0.8941 (mm) cc_final: 0.8471 (tp) REVERT: D 262 GLN cc_start: 0.9597 (tt0) cc_final: 0.9155 (tm-30) REVERT: D 341 ASN cc_start: 0.8944 (m-40) cc_final: 0.8526 (m110) REVERT: D 346 ARG cc_start: 0.9290 (ttm110) cc_final: 0.8354 (ptp-110) REVERT: D 397 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.7979 (tmm-80) REVERT: D 400 LYS cc_start: 0.9562 (mmpt) cc_final: 0.9277 (mmpt) REVERT: D 423 ASP cc_start: 0.8716 (p0) cc_final: 0.8403 (p0) REVERT: D 427 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: D 471 SER cc_start: 0.9291 (t) cc_final: 0.8532 (p) REVERT: D 475 MET cc_start: 0.8958 (mmp) cc_final: 0.8706 (mmp) REVERT: D 504 LEU cc_start: 0.9244 (tp) cc_final: 0.8890 (tp) REVERT: D 505 HIS cc_start: 0.9392 (p-80) cc_final: 0.9119 (p-80) REVERT: D 510 GLN cc_start: 0.7928 (mp10) cc_final: 0.7529 (mp-120) REVERT: D 515 MET cc_start: 0.8662 (mmp) cc_final: 0.8335 (mmm) REVERT: D 527 LEU cc_start: 0.9390 (mt) cc_final: 0.9108 (mt) REVERT: D 552 GLN cc_start: 0.8239 (mp10) cc_final: 0.7914 (mp10) REVERT: D 560 LEU cc_start: 0.9557 (tp) cc_final: 0.9356 (tp) REVERT: D 563 ASN cc_start: 0.8887 (m-40) cc_final: 0.8587 (m-40) REVERT: D 576 MET cc_start: 0.9052 (ppp) cc_final: 0.8728 (ppp) REVERT: D 581 MET cc_start: 0.8845 (mtm) cc_final: 0.8231 (mtm) REVERT: D 633 ILE cc_start: 0.9443 (pt) cc_final: 0.9237 (pt) REVERT: D 641 ARG cc_start: 0.8919 (tpt-90) cc_final: 0.8662 (tpp80) REVERT: D 646 ILE cc_start: 0.9754 (mm) cc_final: 0.9440 (mm) REVERT: D 698 ASN cc_start: 0.9415 (t0) cc_final: 0.9208 (t0) REVERT: D 757 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8922 (tm-30) REVERT: D 779 LYS cc_start: 0.9630 (pttm) cc_final: 0.9345 (pttm) REVERT: D 780 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8867 (mm-30) REVERT: D 784 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9088 (mm-30) REVERT: D 832 ILE cc_start: 0.8994 (mm) cc_final: 0.8692 (mm) REVERT: D 838 SER cc_start: 0.7744 (m) cc_final: 0.7259 (p) REVERT: D 844 LEU cc_start: 0.8763 (mm) cc_final: 0.7830 (tp) REVERT: D 854 HIS cc_start: 0.9061 (m-70) cc_final: 0.8744 (m170) REVERT: D 862 ASP cc_start: 0.9072 (t0) cc_final: 0.8865 (t0) REVERT: D 866 ARG cc_start: 0.9255 (ptt180) cc_final: 0.8380 (ptm160) REVERT: D 928 ASP cc_start: 0.8566 (m-30) cc_final: 0.8168 (m-30) REVERT: D 1060 ARG cc_start: 0.8730 (mmp-170) cc_final: 0.8392 (mmm160) REVERT: D 1112 MET cc_start: 0.9147 (tpt) cc_final: 0.8802 (tpp) REVERT: D 1125 GLN cc_start: 0.8988 (mt0) cc_final: 0.8727 (mp10) REVERT: D 1136 ARG cc_start: 0.9285 (mtm110) cc_final: 0.8981 (ptp-170) REVERT: D 1139 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8869 (tp-100) REVERT: D 1151 ASP cc_start: 0.8632 (t0) cc_final: 0.8257 (t0) REVERT: D 1183 ARG cc_start: 0.9316 (ptp-110) cc_final: 0.8917 (ptp-170) REVERT: D 1244 LYS cc_start: 0.9276 (mmpt) cc_final: 0.8901 (tppt) REVERT: E 46 ARG cc_start: 0.9167 (mpt90) cc_final: 0.8630 (mtt90) REVERT: E 50 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9171 (mtpt) REVERT: E 62 ARG cc_start: 0.8828 (mtt-85) cc_final: 0.8147 (mmt180) REVERT: E 99 ILE cc_start: 0.9735 (OUTLIER) cc_final: 0.9503 (mp) REVERT: F 213 ARG cc_start: 0.8652 (ppt170) cc_final: 0.8312 (ttp80) REVERT: F 258 TYR cc_start: 0.9120 (t80) cc_final: 0.8835 (t80) REVERT: F 282 MET cc_start: 0.9199 (mpp) cc_final: 0.8915 (ptp) REVERT: F 315 MET cc_start: 0.7307 (mpp) cc_final: 0.7095 (mpp) REVERT: F 334 LYS cc_start: 0.8534 (mtpt) cc_final: 0.7878 (mmmt) REVERT: F 352 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8512 (mtm180) REVERT: F 372 MET cc_start: 0.9575 (mmp) cc_final: 0.9323 (mmm) REVERT: F 441 ASP cc_start: 0.8505 (t0) cc_final: 0.7841 (t0) REVERT: F 457 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8784 (mt0) REVERT: F 490 ASP cc_start: 0.8880 (m-30) cc_final: 0.8665 (p0) REVERT: J 54 TRP cc_start: 0.8752 (t-100) cc_final: 0.8500 (t-100) REVERT: J 86 LEU cc_start: 0.9632 (tp) cc_final: 0.9332 (mt) REVERT: M 34 TYR cc_start: 0.9361 (m-80) cc_final: 0.8663 (m-80) REVERT: M 156 GLU cc_start: 0.9754 (tm-30) cc_final: 0.9415 (mm-30) outliers start: 5 outliers final: 0 residues processed: 985 average time/residue: 0.1984 time to fit residues: 304.2634 Evaluate side-chains 813 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 811 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 179 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 318 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN C 442 GLN C 729 HIS D 233 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076069 restraints weight = 98520.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079218 restraints weight = 55020.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081358 restraints weight = 36662.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082909 restraints weight = 27291.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083856 restraints weight = 22016.093| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30158 Z= 0.147 Angle : 0.706 25.818 41380 Z= 0.365 Chirality : 0.052 1.946 4726 Planarity : 0.006 0.255 5007 Dihedral : 17.244 179.999 5172 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 0.14 % Allowed : 3.61 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3441 helix: 0.38 (0.14), residues: 1400 sheet: -0.41 (0.27), residues: 377 loop : -1.11 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1030 TYR 0.029 0.002 TYR F 346 PHE 0.018 0.002 PHE C 300 TRP 0.054 0.002 TRP M 112 HIS 0.009 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00323 (30150) covalent geometry : angle 0.70416 (41368) hydrogen bonds : bond 0.04148 ( 1389) hydrogen bonds : angle 5.03408 ( 3855) metal coordination : bond 0.00722 ( 8) metal coordination : angle 2.75922 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 972 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.6679 (m-80) cc_final: 0.6304 (m-10) REVERT: A 34 LEU cc_start: 0.9454 (tp) cc_final: 0.9072 (tp) REVERT: A 125 ILE cc_start: 0.9723 (mm) cc_final: 0.9467 (mm) REVERT: A 134 LEU cc_start: 0.9422 (tp) cc_final: 0.9221 (tp) REVERT: A 138 LEU cc_start: 0.9442 (mp) cc_final: 0.9121 (mp) REVERT: A 151 GLN cc_start: 0.8270 (mp-120) cc_final: 0.7888 (pm20) REVERT: A 176 TYR cc_start: 0.8094 (p90) cc_final: 0.7833 (p90) REVERT: A 179 ASP cc_start: 0.8983 (t0) cc_final: 0.8759 (t0) REVERT: A 197 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8395 (mt-10) REVERT: A 208 LEU cc_start: 0.9602 (mm) cc_final: 0.9344 (mp) REVERT: A 219 PHE cc_start: 0.7945 (m-80) cc_final: 0.7616 (m-80) REVERT: B 14 LEU cc_start: 0.9355 (mt) cc_final: 0.8976 (mt) REVERT: B 20 GLN cc_start: 0.8674 (mp10) cc_final: 0.8002 (mp10) REVERT: B 39 ARG cc_start: 0.9323 (tmm-80) cc_final: 0.8395 (ttp80) REVERT: B 40 ARG cc_start: 0.9219 (mmp-170) cc_final: 0.8822 (mmm160) REVERT: B 42 LEU cc_start: 0.9815 (mt) cc_final: 0.9591 (mt) REVERT: B 95 MET cc_start: 0.7708 (tpt) cc_final: 0.7295 (tpp) REVERT: B 120 ASN cc_start: 0.9423 (t0) cc_final: 0.8998 (t0) REVERT: B 138 LEU cc_start: 0.9144 (mt) cc_final: 0.8896 (mt) REVERT: B 151 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8610 (tm-30) REVERT: B 165 ASP cc_start: 0.9032 (m-30) cc_final: 0.8763 (m-30) REVERT: B 213 LYS cc_start: 0.9590 (tptp) cc_final: 0.9375 (tppt) REVERT: B 217 GLU cc_start: 0.9452 (pt0) cc_final: 0.9193 (tm-30) REVERT: B 219 PHE cc_start: 0.9121 (m-80) cc_final: 0.8672 (m-80) REVERT: C 59 ASP cc_start: 0.9451 (m-30) cc_final: 0.9190 (m-30) REVERT: C 87 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8731 (mp0) REVERT: C 93 LEU cc_start: 0.9405 (tp) cc_final: 0.9163 (tp) REVERT: C 177 SER cc_start: 0.8987 (m) cc_final: 0.8683 (t) REVERT: C 199 LEU cc_start: 0.9270 (pp) cc_final: 0.9008 (mt) REVERT: C 239 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7853 (tppt) REVERT: C 263 GLU cc_start: 0.8823 (mp0) cc_final: 0.8552 (mp0) REVERT: C 279 ARG cc_start: 0.9596 (tmt170) cc_final: 0.9384 (ptp-110) REVERT: C 308 LEU cc_start: 0.9476 (mm) cc_final: 0.9261 (mm) REVERT: C 396 MET cc_start: 0.9133 (tpp) cc_final: 0.8684 (tpt) REVERT: C 441 ASP cc_start: 0.9081 (m-30) cc_final: 0.8789 (m-30) REVERT: C 442 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8670 (tp-100) REVERT: C 466 GLU cc_start: 0.9160 (pm20) cc_final: 0.8824 (pm20) REVERT: C 482 ARG cc_start: 0.8831 (mtt180) cc_final: 0.7650 (mmt90) REVERT: C 483 MET cc_start: 0.8288 (tpp) cc_final: 0.7900 (tpp) REVERT: C 511 PHE cc_start: 0.9035 (m-80) cc_final: 0.8228 (m-10) REVERT: C 516 TYR cc_start: 0.8671 (m-80) cc_final: 0.7571 (m-80) REVERT: C 531 LEU cc_start: 0.8718 (mt) cc_final: 0.8142 (mt) REVERT: C 543 GLN cc_start: 0.7749 (tt0) cc_final: 0.7323 (tm-30) REVERT: C 585 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8195 (tp40) REVERT: C 601 ASP cc_start: 0.9260 (t0) cc_final: 0.8748 (p0) REVERT: C 613 ARG cc_start: 0.9298 (mtm110) cc_final: 0.8679 (mtm-85) REVERT: C 620 ARG cc_start: 0.9324 (tpm170) cc_final: 0.9046 (tpm170) REVERT: C 744 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8955 (mp0) REVERT: C 846 LYS cc_start: 0.9313 (tptt) cc_final: 0.8920 (tppt) REVERT: C 873 VAL cc_start: 0.9105 (t) cc_final: 0.8750 (p) REVERT: C 892 LYS cc_start: 0.9291 (ptpt) cc_final: 0.8853 (ptpt) REVERT: C 904 MET cc_start: 0.9007 (tpp) cc_final: 0.8576 (ttm) REVERT: C 907 LEU cc_start: 0.8610 (tp) cc_final: 0.8319 (tp) REVERT: C 926 MET cc_start: 0.9035 (tpt) cc_final: 0.8591 (tpp) REVERT: C 933 GLU cc_start: 0.8952 (tt0) cc_final: 0.8640 (tt0) REVERT: C 944 TRP cc_start: 0.8859 (p90) cc_final: 0.8315 (p90) REVERT: C 962 GLU cc_start: 0.8418 (mp0) cc_final: 0.8201 (mp0) REVERT: C 963 LEU cc_start: 0.8225 (mt) cc_final: 0.7888 (mt) REVERT: C 1021 TYR cc_start: 0.8256 (m-80) cc_final: 0.8043 (m-80) REVERT: C 1031 MET cc_start: 0.8805 (mtm) cc_final: 0.8289 (mtm) REVERT: C 1035 HIS cc_start: 0.7192 (m90) cc_final: 0.6807 (m-70) REVERT: C 1036 LEU cc_start: 0.8998 (mt) cc_final: 0.8705 (mt) REVERT: C 1039 ASP cc_start: 0.9181 (m-30) cc_final: 0.8890 (m-30) REVERT: C 1040 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7675 (mptt) REVERT: C 1051 MET cc_start: 0.9014 (tpp) cc_final: 0.8799 (mmm) REVERT: C 1076 MET cc_start: 0.8894 (ttm) cc_final: 0.8645 (ttm) REVERT: C 1077 GLN cc_start: 0.9421 (mt0) cc_final: 0.9077 (mt0) REVERT: C 1086 GLN cc_start: 0.9498 (pt0) cc_final: 0.9238 (pt0) REVERT: C 1090 THR cc_start: 0.9100 (m) cc_final: 0.8856 (p) REVERT: C 1091 ILE cc_start: 0.9050 (pt) cc_final: 0.8848 (pt) REVERT: C 1104 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8897 (mp0) REVERT: C 1121 PHE cc_start: 0.9579 (t80) cc_final: 0.9369 (t80) REVERT: C 1128 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mt) REVERT: C 1138 LEU cc_start: 0.8653 (mt) cc_final: 0.8408 (tp) REVERT: D 29 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8926 (ptpp) REVERT: D 52 PHE cc_start: 0.8139 (m-80) cc_final: 0.6755 (m-10) REVERT: D 64 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8353 (mtpt) REVERT: D 66 LYS cc_start: 0.9294 (ptpp) cc_final: 0.9042 (mmmt) REVERT: D 118 LEU cc_start: 0.9400 (mm) cc_final: 0.8945 (mm) REVERT: D 119 ASP cc_start: 0.8564 (t70) cc_final: 0.8296 (t70) REVERT: D 120 LEU cc_start: 0.8847 (mm) cc_final: 0.8369 (tp) REVERT: D 262 GLN cc_start: 0.9596 (tt0) cc_final: 0.9176 (tp40) REVERT: D 341 ASN cc_start: 0.8984 (m-40) cc_final: 0.8526 (m110) REVERT: D 346 ARG cc_start: 0.9319 (ttm110) cc_final: 0.8387 (ptp-110) REVERT: D 386 ARG cc_start: 0.7893 (tpt170) cc_final: 0.7554 (mmm160) REVERT: D 427 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.7726 (ttm-80) REVERT: D 471 SER cc_start: 0.9179 (t) cc_final: 0.8417 (p) REVERT: D 475 MET cc_start: 0.9011 (mmp) cc_final: 0.8759 (mmp) REVERT: D 498 LEU cc_start: 0.8882 (mt) cc_final: 0.8673 (mt) REVERT: D 503 THR cc_start: 0.8686 (p) cc_final: 0.7982 (p) REVERT: D 504 LEU cc_start: 0.9160 (tp) cc_final: 0.8654 (tp) REVERT: D 505 HIS cc_start: 0.9359 (p-80) cc_final: 0.8782 (p-80) REVERT: D 506 ARG cc_start: 0.9257 (ttt180) cc_final: 0.8944 (tpt-90) REVERT: D 510 GLN cc_start: 0.8362 (mp10) cc_final: 0.7727 (mp10) REVERT: D 515 MET cc_start: 0.8583 (mmp) cc_final: 0.8220 (mmm) REVERT: D 518 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6221 (mm-30) REVERT: D 523 GLN cc_start: 0.8743 (tt0) cc_final: 0.8059 (tp40) REVERT: D 527 LEU cc_start: 0.9342 (mt) cc_final: 0.9037 (mt) REVERT: D 529 CYS cc_start: 0.8999 (t) cc_final: 0.8646 (t) REVERT: D 532 PHE cc_start: 0.7988 (m-80) cc_final: 0.7732 (m-80) REVERT: D 545 LEU cc_start: 0.9354 (tp) cc_final: 0.9142 (tp) REVERT: D 560 LEU cc_start: 0.9522 (tp) cc_final: 0.9258 (tp) REVERT: D 576 MET cc_start: 0.9028 (ppp) cc_final: 0.8681 (ppp) REVERT: D 581 MET cc_start: 0.8787 (mtm) cc_final: 0.8261 (mtm) REVERT: D 641 ARG cc_start: 0.8975 (tpt-90) cc_final: 0.8671 (tpp80) REVERT: D 672 MET cc_start: 0.9370 (ttp) cc_final: 0.9104 (ttp) REVERT: D 698 ASN cc_start: 0.9443 (t0) cc_final: 0.9239 (t0) REVERT: D 706 MET cc_start: 0.8800 (pmm) cc_final: 0.8321 (pmm) REVERT: D 757 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8914 (tm-30) REVERT: D 779 LYS cc_start: 0.9627 (pttm) cc_final: 0.9382 (pttm) REVERT: D 780 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8869 (mm-30) REVERT: D 784 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9087 (mm-30) REVERT: D 840 PHE cc_start: 0.9090 (m-80) cc_final: 0.8411 (m-80) REVERT: D 844 LEU cc_start: 0.8763 (mm) cc_final: 0.7736 (tp) REVERT: D 866 ARG cc_start: 0.9112 (ptt180) cc_final: 0.8651 (ptm160) REVERT: D 928 ASP cc_start: 0.8498 (m-30) cc_final: 0.8143 (m-30) REVERT: D 1001 GLN cc_start: 0.9460 (tt0) cc_final: 0.9115 (tp-100) REVERT: D 1060 ARG cc_start: 0.8788 (mmp-170) cc_final: 0.8428 (mmm160) REVERT: D 1133 HIS cc_start: 0.9203 (t70) cc_final: 0.8904 (t70) REVERT: D 1136 ARG cc_start: 0.9292 (mtm110) cc_final: 0.8739 (ptp-170) REVERT: D 1137 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8853 (mm-30) REVERT: D 1139 GLN cc_start: 0.9242 (tp-100) cc_final: 0.8871 (tp-100) REVERT: D 1140 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8806 (mt-10) REVERT: D 1151 ASP cc_start: 0.8584 (t0) cc_final: 0.8206 (t0) REVERT: D 1183 ARG cc_start: 0.9314 (ptp-110) cc_final: 0.8965 (ptp90) REVERT: D 1249 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8631 (ttpt) REVERT: E 46 ARG cc_start: 0.9106 (mpt90) cc_final: 0.8659 (mtt90) REVERT: E 50 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9152 (mtpt) REVERT: E 65 ASN cc_start: 0.9203 (t0) cc_final: 0.8879 (t0) REVERT: E 66 ASP cc_start: 0.8854 (m-30) cc_final: 0.8374 (m-30) REVERT: E 99 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9428 (mp) REVERT: E 108 GLU cc_start: 0.9273 (pm20) cc_final: 0.7960 (tm-30) REVERT: F 213 ARG cc_start: 0.8645 (ppt170) cc_final: 0.8361 (ttp80) REVERT: F 282 MET cc_start: 0.9221 (mpp) cc_final: 0.9009 (ptp) REVERT: F 315 MET cc_start: 0.6884 (mpp) cc_final: 0.6591 (mpp) REVERT: F 352 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8401 (mtm180) REVERT: F 357 ARG cc_start: 0.9632 (tmt170) cc_final: 0.9391 (ttp80) REVERT: F 372 MET cc_start: 0.9573 (mmp) cc_final: 0.9346 (mmm) REVERT: J 54 TRP cc_start: 0.8753 (t-100) cc_final: 0.8521 (t-100) REVERT: J 91 ILE cc_start: 0.8799 (pt) cc_final: 0.8539 (pt) REVERT: M 34 TYR cc_start: 0.9402 (m-80) cc_final: 0.8709 (m-80) REVERT: M 156 GLU cc_start: 0.9724 (tm-30) cc_final: 0.9429 (mm-30) outliers start: 4 outliers final: 2 residues processed: 974 average time/residue: 0.2037 time to fit residues: 306.7779 Evaluate side-chains 800 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 796 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 33 optimal weight: 0.0170 chunk 230 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN D1160 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072619 restraints weight = 99917.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075589 restraints weight = 56488.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077643 restraints weight = 37933.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078961 restraints weight = 28416.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079970 restraints weight = 23223.414| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30158 Z= 0.211 Angle : 0.752 25.825 41380 Z= 0.390 Chirality : 0.052 1.922 4726 Planarity : 0.006 0.094 5007 Dihedral : 17.337 178.369 5172 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3441 helix: 0.25 (0.14), residues: 1394 sheet: -0.63 (0.25), residues: 410 loop : -1.10 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 229 TYR 0.022 0.002 TYR E 56 PHE 0.037 0.002 PHE C1063 TRP 0.060 0.003 TRP M 112 HIS 0.013 0.002 HIS J 81 Details of bonding type rmsd covalent geometry : bond 0.00451 (30150) covalent geometry : angle 0.74766 (41368) hydrogen bonds : bond 0.04593 ( 1389) hydrogen bonds : angle 5.17963 ( 3855) metal coordination : bond 0.01505 ( 8) metal coordination : angle 4.58873 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 887 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8722 (tp30) cc_final: 0.7934 (tp30) REVERT: A 30 PHE cc_start: 0.7105 (m-80) cc_final: 0.6136 (m-80) REVERT: A 34 LEU cc_start: 0.9483 (tp) cc_final: 0.9108 (tp) REVERT: A 38 LEU cc_start: 0.9809 (mt) cc_final: 0.9567 (mt) REVERT: A 83 LEU cc_start: 0.9650 (tp) cc_final: 0.9445 (mm) REVERT: A 125 ILE cc_start: 0.9629 (mm) cc_final: 0.9385 (mm) REVERT: A 134 LEU cc_start: 0.9406 (tp) cc_final: 0.9197 (tp) REVERT: A 138 LEU cc_start: 0.9364 (mp) cc_final: 0.9026 (mp) REVERT: A 141 GLU cc_start: 0.8228 (tp30) cc_final: 0.7640 (tp30) REVERT: A 151 GLN cc_start: 0.8349 (mp-120) cc_final: 0.8073 (pm20) REVERT: A 179 ASP cc_start: 0.9024 (t0) cc_final: 0.8763 (t0) REVERT: A 197 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 208 LEU cc_start: 0.9617 (mm) cc_final: 0.9401 (mm) REVERT: A 219 PHE cc_start: 0.8218 (m-80) cc_final: 0.7888 (m-80) REVERT: B 12 ASP cc_start: 0.9286 (t70) cc_final: 0.8907 (t0) REVERT: B 18 ARG cc_start: 0.9210 (ptt180) cc_final: 0.8945 (ttp-110) REVERT: B 20 GLN cc_start: 0.8565 (mp10) cc_final: 0.7863 (mp10) REVERT: B 39 ARG cc_start: 0.9342 (tmm-80) cc_final: 0.8790 (ttp80) REVERT: B 42 LEU cc_start: 0.9807 (mt) cc_final: 0.9586 (mt) REVERT: B 95 MET cc_start: 0.7671 (tpt) cc_final: 0.7209 (tpp) REVERT: B 120 ASN cc_start: 0.9448 (t0) cc_final: 0.9071 (t0) REVERT: B 138 LEU cc_start: 0.9081 (mt) cc_final: 0.8857 (mt) REVERT: B 151 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8788 (tm-30) REVERT: B 177 LYS cc_start: 0.8563 (mppt) cc_final: 0.8339 (mmtm) REVERT: B 213 LYS cc_start: 0.9606 (tptp) cc_final: 0.9384 (tppt) REVERT: B 217 GLU cc_start: 0.9451 (pt0) cc_final: 0.9139 (tm-30) REVERT: B 219 PHE cc_start: 0.9239 (m-80) cc_final: 0.8878 (m-80) REVERT: C 59 ASP cc_start: 0.9452 (m-30) cc_final: 0.9193 (m-30) REVERT: C 93 LEU cc_start: 0.9417 (tp) cc_final: 0.9137 (tp) REVERT: C 239 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7927 (tppt) REVERT: C 279 ARG cc_start: 0.9600 (tmt170) cc_final: 0.9356 (ttp80) REVERT: C 376 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7741 (mtp85) REVERT: C 386 GLN cc_start: 0.9403 (pt0) cc_final: 0.9045 (pt0) REVERT: C 482 ARG cc_start: 0.8686 (mtt180) cc_final: 0.7453 (mmt90) REVERT: C 483 MET cc_start: 0.8465 (tpp) cc_final: 0.7839 (tpp) REVERT: C 511 PHE cc_start: 0.9168 (m-80) cc_final: 0.8328 (m-10) REVERT: C 543 GLN cc_start: 0.7967 (tt0) cc_final: 0.7233 (tt0) REVERT: C 585 GLN cc_start: 0.9092 (tp-100) cc_final: 0.8265 (tp-100) REVERT: C 601 ASP cc_start: 0.9246 (t0) cc_final: 0.8873 (p0) REVERT: C 620 ARG cc_start: 0.9348 (tpm170) cc_final: 0.8973 (tpm170) REVERT: C 672 MET cc_start: 0.6780 (ppp) cc_final: 0.6356 (ppp) REVERT: C 680 HIS cc_start: 0.8130 (m90) cc_final: 0.7779 (m-70) REVERT: C 753 GLU cc_start: 0.8522 (mp0) cc_final: 0.8250 (mp0) REVERT: C 846 LYS cc_start: 0.9303 (tptt) cc_final: 0.8896 (tppt) REVERT: C 873 VAL cc_start: 0.9184 (t) cc_final: 0.8439 (p) REVERT: C 892 LYS cc_start: 0.9328 (ptpt) cc_final: 0.8926 (ptpt) REVERT: C 926 MET cc_start: 0.9036 (tpt) cc_final: 0.8671 (tpp) REVERT: C 930 GLN cc_start: 0.9416 (pt0) cc_final: 0.9137 (pt0) REVERT: C 933 GLU cc_start: 0.8848 (tt0) cc_final: 0.8477 (tt0) REVERT: C 944 TRP cc_start: 0.8807 (p90) cc_final: 0.8349 (p90) REVERT: C 962 GLU cc_start: 0.8393 (mp0) cc_final: 0.8113 (mp0) REVERT: C 1031 MET cc_start: 0.8730 (mtm) cc_final: 0.8270 (mtm) REVERT: C 1033 LEU cc_start: 0.9592 (mp) cc_final: 0.9359 (mt) REVERT: C 1036 LEU cc_start: 0.8919 (mt) cc_final: 0.8673 (mt) REVERT: C 1039 ASP cc_start: 0.9186 (m-30) cc_final: 0.8816 (m-30) REVERT: C 1040 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7900 (mptt) REVERT: C 1051 MET cc_start: 0.9091 (tpp) cc_final: 0.8726 (mmm) REVERT: C 1071 MET cc_start: 0.7635 (pmm) cc_final: 0.6599 (pmm) REVERT: C 1076 MET cc_start: 0.9015 (ttm) cc_final: 0.8811 (ttm) REVERT: C 1077 GLN cc_start: 0.9491 (mt0) cc_final: 0.9061 (mt0) REVERT: C 1084 THR cc_start: 0.9532 (t) cc_final: 0.9207 (t) REVERT: C 1090 THR cc_start: 0.9117 (m) cc_final: 0.8858 (p) REVERT: C 1091 ILE cc_start: 0.9104 (pt) cc_final: 0.8864 (pt) REVERT: C 1124 LEU cc_start: 0.9622 (tt) cc_final: 0.9254 (tt) REVERT: C 1128 LEU cc_start: 0.9342 (mt) cc_final: 0.9085 (mt) REVERT: D 29 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8863 (ptpp) REVERT: D 64 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8376 (mtpt) REVERT: D 66 LYS cc_start: 0.9322 (ptpp) cc_final: 0.9026 (mmmt) REVERT: D 143 MET cc_start: 0.9123 (pmm) cc_final: 0.8852 (pmm) REVERT: D 147 GLU cc_start: 0.9479 (tp30) cc_final: 0.9149 (mm-30) REVERT: D 262 GLN cc_start: 0.9602 (tt0) cc_final: 0.9181 (tp40) REVERT: D 341 ASN cc_start: 0.9062 (m-40) cc_final: 0.8609 (m110) REVERT: D 386 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7809 (mmm160) REVERT: D 397 ARG cc_start: 0.8989 (tmm-80) cc_final: 0.8532 (tmm-80) REVERT: D 427 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.7539 (ttm-80) REVERT: D 436 LEU cc_start: 0.8916 (mm) cc_final: 0.8436 (tp) REVERT: D 471 SER cc_start: 0.9257 (t) cc_final: 0.8374 (m) REVERT: D 475 MET cc_start: 0.9066 (mmp) cc_final: 0.8842 (mmp) REVERT: D 503 THR cc_start: 0.8877 (p) cc_final: 0.8270 (p) REVERT: D 504 LEU cc_start: 0.9200 (tp) cc_final: 0.8826 (tp) REVERT: D 505 HIS cc_start: 0.9325 (p-80) cc_final: 0.9084 (p-80) REVERT: D 510 GLN cc_start: 0.8528 (mp10) cc_final: 0.7933 (mp10) REVERT: D 515 MET cc_start: 0.8727 (mmp) cc_final: 0.8447 (mmm) REVERT: D 527 LEU cc_start: 0.9268 (mt) cc_final: 0.9013 (mt) REVERT: D 552 GLN cc_start: 0.8425 (mp10) cc_final: 0.7770 (mp-120) REVERT: D 576 MET cc_start: 0.8944 (ppp) cc_final: 0.8664 (ppp) REVERT: D 581 MET cc_start: 0.8901 (mtm) cc_final: 0.8493 (mtm) REVERT: D 641 ARG cc_start: 0.8998 (tpt-90) cc_final: 0.8690 (tpp80) REVERT: D 672 MET cc_start: 0.9365 (ttp) cc_final: 0.9131 (ttp) REVERT: D 698 ASN cc_start: 0.9419 (t0) cc_final: 0.9201 (t0) REVERT: D 706 MET cc_start: 0.8802 (pmm) cc_final: 0.8325 (pmm) REVERT: D 780 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8633 (tt0) REVERT: D 784 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9040 (mm-30) REVERT: D 820 MET cc_start: 0.8872 (tmm) cc_final: 0.8514 (tmm) REVERT: D 840 PHE cc_start: 0.9064 (m-80) cc_final: 0.8592 (m-80) REVERT: D 854 HIS cc_start: 0.9040 (m-70) cc_final: 0.8781 (m170) REVERT: D 866 ARG cc_start: 0.9135 (ptt180) cc_final: 0.8671 (ptm160) REVERT: D 898 VAL cc_start: 0.9392 (t) cc_final: 0.8981 (p) REVERT: D 928 ASP cc_start: 0.8472 (m-30) cc_final: 0.8135 (m-30) REVERT: D 1060 ARG cc_start: 0.8848 (mmp-170) cc_final: 0.8612 (mmm160) REVERT: D 1137 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8980 (mm-30) REVERT: D 1139 GLN cc_start: 0.9270 (tp-100) cc_final: 0.8895 (tp-100) REVERT: D 1140 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8851 (mt-10) REVERT: D 1151 ASP cc_start: 0.8684 (t0) cc_final: 0.8310 (t0) REVERT: D 1183 ARG cc_start: 0.9372 (ptp-110) cc_final: 0.8828 (ptp-170) REVERT: D 1231 ARG cc_start: 0.9093 (ptt90) cc_final: 0.8796 (ptt90) REVERT: D 1244 LYS cc_start: 0.9274 (mmpt) cc_final: 0.8843 (tppt) REVERT: E 50 LYS cc_start: 0.9562 (mtpt) cc_final: 0.9250 (mtpt) REVERT: E 65 ASN cc_start: 0.9010 (t0) cc_final: 0.8716 (t0) REVERT: E 78 TYR cc_start: 0.8327 (m-10) cc_final: 0.8026 (m-10) REVERT: E 107 THR cc_start: 0.8880 (p) cc_final: 0.8523 (p) REVERT: E 108 GLU cc_start: 0.9188 (pm20) cc_final: 0.7939 (tm-30) REVERT: F 213 ARG cc_start: 0.8675 (ppt170) cc_final: 0.8198 (ttp80) REVERT: F 258 TYR cc_start: 0.9235 (t80) cc_final: 0.8988 (t80) REVERT: F 333 GLU cc_start: 0.8392 (tt0) cc_final: 0.7841 (tm-30) REVERT: F 352 ARG cc_start: 0.8739 (mtp-110) cc_final: 0.8437 (mtm180) REVERT: F 357 ARG cc_start: 0.9608 (tmt170) cc_final: 0.9356 (tmt-80) REVERT: J 54 TRP cc_start: 0.8773 (t-100) cc_final: 0.8563 (t-100) REVERT: J 84 MET cc_start: 0.9331 (mpp) cc_final: 0.8752 (mpp) REVERT: J 86 LEU cc_start: 0.9626 (tp) cc_final: 0.9336 (mt) REVERT: J 91 ILE cc_start: 0.8801 (pt) cc_final: 0.8429 (pt) REVERT: M 34 TYR cc_start: 0.9387 (m-80) cc_final: 0.8726 (m-80) REVERT: M 156 GLU cc_start: 0.9725 (tm-30) cc_final: 0.9432 (mm-30) outliers start: 0 outliers final: 0 residues processed: 887 average time/residue: 0.1995 time to fit residues: 273.3969 Evaluate side-chains 750 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 750 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 286 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 289 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN C 612 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073198 restraints weight = 99935.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076148 restraints weight = 56177.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078264 restraints weight = 37787.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079683 restraints weight = 28101.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080621 restraints weight = 22832.287| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 30158 Z= 0.179 Angle : 0.727 26.159 41380 Z= 0.379 Chirality : 0.053 1.931 4726 Planarity : 0.005 0.082 5007 Dihedral : 17.302 178.274 5172 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.31 % Favored : 93.66 % Rotamer: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3441 helix: 0.15 (0.14), residues: 1408 sheet: -0.69 (0.26), residues: 385 loop : -1.01 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 345 TYR 0.022 0.002 TYR E 56 PHE 0.025 0.002 PHE C1063 TRP 0.048 0.002 TRP M 112 HIS 0.014 0.002 HIS J 81 Details of bonding type rmsd covalent geometry : bond 0.00390 (30150) covalent geometry : angle 0.72411 (41368) hydrogen bonds : bond 0.04288 ( 1389) hydrogen bonds : angle 5.25617 ( 3855) metal coordination : bond 0.01008 ( 8) metal coordination : angle 3.77523 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 882 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8770 (tp30) cc_final: 0.7929 (tp30) REVERT: A 30 PHE cc_start: 0.6903 (m-80) cc_final: 0.5998 (m-80) REVERT: A 34 LEU cc_start: 0.9432 (tp) cc_final: 0.9071 (tp) REVERT: A 72 ASP cc_start: 0.8930 (m-30) cc_final: 0.8615 (m-30) REVERT: A 83 LEU cc_start: 0.9674 (tp) cc_final: 0.9377 (tp) REVERT: A 138 LEU cc_start: 0.9362 (mp) cc_final: 0.9036 (mp) REVERT: A 141 GLU cc_start: 0.8219 (tp30) cc_final: 0.7637 (tp30) REVERT: A 151 GLN cc_start: 0.8333 (mp-120) cc_final: 0.8071 (pm20) REVERT: A 179 ASP cc_start: 0.9085 (t0) cc_final: 0.8814 (t0) REVERT: A 197 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 219 PHE cc_start: 0.8220 (m-80) cc_final: 0.7886 (m-80) REVERT: B 12 ASP cc_start: 0.9329 (t70) cc_final: 0.8997 (t0) REVERT: B 20 GLN cc_start: 0.8710 (mp10) cc_final: 0.8170 (mp10) REVERT: B 39 ARG cc_start: 0.9342 (tmm-80) cc_final: 0.8800 (ttp80) REVERT: B 42 LEU cc_start: 0.9807 (mt) cc_final: 0.9579 (mt) REVERT: B 95 MET cc_start: 0.7772 (tpt) cc_final: 0.7478 (tpp) REVERT: B 120 ASN cc_start: 0.9500 (t0) cc_final: 0.9156 (t0) REVERT: B 151 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8794 (tm-30) REVERT: B 213 LYS cc_start: 0.9599 (tptp) cc_final: 0.9378 (tppt) REVERT: B 217 GLU cc_start: 0.9456 (pt0) cc_final: 0.9148 (tm-30) REVERT: B 219 PHE cc_start: 0.9267 (m-80) cc_final: 0.8903 (m-80) REVERT: C 59 ASP cc_start: 0.9460 (m-30) cc_final: 0.9199 (m-30) REVERT: C 93 LEU cc_start: 0.9468 (tp) cc_final: 0.9119 (tp) REVERT: C 157 PHE cc_start: 0.8716 (t80) cc_final: 0.8449 (t80) REVERT: C 213 GLU cc_start: 0.7889 (mm-30) cc_final: 0.6984 (mm-30) REVERT: C 239 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7794 (tppt) REVERT: C 263 GLU cc_start: 0.8815 (mp0) cc_final: 0.8612 (mp0) REVERT: C 279 ARG cc_start: 0.9585 (tmt170) cc_final: 0.9359 (ttp80) REVERT: C 308 LEU cc_start: 0.9422 (tp) cc_final: 0.9217 (tp) REVERT: C 376 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7652 (mtp85) REVERT: C 396 MET cc_start: 0.8996 (tpp) cc_final: 0.8645 (tpt) REVERT: C 410 GLU cc_start: 0.8532 (tp30) cc_final: 0.8266 (tp30) REVERT: C 442 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8829 (tp-100) REVERT: C 482 ARG cc_start: 0.8485 (mtt180) cc_final: 0.7108 (mmt90) REVERT: C 483 MET cc_start: 0.8376 (tpp) cc_final: 0.7813 (tpp) REVERT: C 511 PHE cc_start: 0.9105 (m-80) cc_final: 0.8293 (m-10) REVERT: C 513 GLU cc_start: 0.7200 (pm20) cc_final: 0.6889 (pm20) REVERT: C 543 GLN cc_start: 0.7721 (tt0) cc_final: 0.7299 (tm-30) REVERT: C 585 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8109 (tp40) REVERT: C 620 ARG cc_start: 0.9356 (tpm170) cc_final: 0.9021 (tpm170) REVERT: C 630 MET cc_start: 0.8752 (mmp) cc_final: 0.8543 (mmp) REVERT: C 680 HIS cc_start: 0.8053 (m90) cc_final: 0.7504 (m90) REVERT: C 846 LYS cc_start: 0.9335 (tptt) cc_final: 0.8912 (tppt) REVERT: C 892 LYS cc_start: 0.9284 (ptpt) cc_final: 0.8828 (ptpt) REVERT: C 933 GLU cc_start: 0.8857 (tt0) cc_final: 0.8443 (tt0) REVERT: C 944 TRP cc_start: 0.8827 (p90) cc_final: 0.8268 (p90) REVERT: C 962 GLU cc_start: 0.8364 (mp0) cc_final: 0.8101 (mp0) REVERT: C 988 LEU cc_start: 0.9540 (mm) cc_final: 0.9244 (mm) REVERT: C 1036 LEU cc_start: 0.9022 (mt) cc_final: 0.8749 (mt) REVERT: C 1039 ASP cc_start: 0.9207 (m-30) cc_final: 0.8860 (m-30) REVERT: C 1040 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7778 (mptt) REVERT: C 1051 MET cc_start: 0.9081 (tpp) cc_final: 0.8684 (mmm) REVERT: C 1071 MET cc_start: 0.7670 (pmm) cc_final: 0.6604 (pmm) REVERT: C 1073 CYS cc_start: 0.9021 (m) cc_final: 0.8808 (m) REVERT: C 1076 MET cc_start: 0.9095 (ttm) cc_final: 0.8760 (ttm) REVERT: C 1086 GLN cc_start: 0.9450 (pt0) cc_final: 0.9153 (pt0) REVERT: C 1090 THR cc_start: 0.9128 (m) cc_final: 0.8864 (p) REVERT: C 1092 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8470 (mtpp) REVERT: C 1121 PHE cc_start: 0.9563 (t80) cc_final: 0.9327 (t80) REVERT: C 1128 LEU cc_start: 0.9399 (mt) cc_final: 0.9197 (mt) REVERT: D 29 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8932 (ptpp) REVERT: D 64 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8400 (mtpt) REVERT: D 66 LYS cc_start: 0.9311 (ptpp) cc_final: 0.9016 (mmmt) REVERT: D 118 LEU cc_start: 0.9379 (mm) cc_final: 0.8952 (mm) REVERT: D 119 ASP cc_start: 0.8584 (t70) cc_final: 0.8165 (t0) REVERT: D 120 LEU cc_start: 0.8930 (mm) cc_final: 0.8493 (tp) REVERT: D 143 MET cc_start: 0.9166 (pmm) cc_final: 0.8884 (pmm) REVERT: D 147 GLU cc_start: 0.9475 (tp30) cc_final: 0.9171 (mm-30) REVERT: D 262 GLN cc_start: 0.9600 (tt0) cc_final: 0.9194 (tm-30) REVERT: D 341 ASN cc_start: 0.9083 (m-40) cc_final: 0.8584 (m110) REVERT: D 364 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 379 ASP cc_start: 0.9469 (t0) cc_final: 0.9263 (t0) REVERT: D 424 TYR cc_start: 0.8673 (m-80) cc_final: 0.8420 (m-10) REVERT: D 427 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7583 (ttm-80) REVERT: D 440 GLN cc_start: 0.8935 (mt0) cc_final: 0.8357 (mt0) REVERT: D 471 SER cc_start: 0.9263 (t) cc_final: 0.8693 (p) REVERT: D 475 MET cc_start: 0.9115 (mmp) cc_final: 0.8870 (mmp) REVERT: D 503 THR cc_start: 0.8787 (p) cc_final: 0.8165 (p) REVERT: D 504 LEU cc_start: 0.9156 (tp) cc_final: 0.8861 (tp) REVERT: D 505 HIS cc_start: 0.9242 (p-80) cc_final: 0.9019 (p-80) REVERT: D 510 GLN cc_start: 0.8516 (mp10) cc_final: 0.8091 (mp10) REVERT: D 515 MET cc_start: 0.8653 (mmp) cc_final: 0.8430 (mmm) REVERT: D 523 GLN cc_start: 0.8681 (tt0) cc_final: 0.8115 (tp40) REVERT: D 527 LEU cc_start: 0.9236 (mt) cc_final: 0.8984 (mt) REVERT: D 532 PHE cc_start: 0.8008 (m-80) cc_final: 0.7506 (m-80) REVERT: D 552 GLN cc_start: 0.8194 (mp10) cc_final: 0.7958 (mp-120) REVERT: D 574 LEU cc_start: 0.8976 (mt) cc_final: 0.8556 (mt) REVERT: D 576 MET cc_start: 0.8947 (ppp) cc_final: 0.8689 (ppp) REVERT: D 581 MET cc_start: 0.8895 (mtm) cc_final: 0.8425 (mtm) REVERT: D 640 LEU cc_start: 0.8922 (mp) cc_final: 0.8507 (mt) REVERT: D 641 ARG cc_start: 0.9101 (tpt-90) cc_final: 0.8769 (tpp80) REVERT: D 667 THR cc_start: 0.9260 (p) cc_final: 0.8937 (t) REVERT: D 672 MET cc_start: 0.9326 (ttp) cc_final: 0.9064 (ttp) REVERT: D 675 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9168 (tm-30) REVERT: D 698 ASN cc_start: 0.9432 (t0) cc_final: 0.9221 (t0) REVERT: D 706 MET cc_start: 0.8816 (pmm) cc_final: 0.8325 (pmm) REVERT: D 717 LYS cc_start: 0.9390 (tmmt) cc_final: 0.8722 (tmmt) REVERT: D 780 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8422 (tt0) REVERT: D 784 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9030 (mm-30) REVERT: D 815 ARG cc_start: 0.9453 (tmm-80) cc_final: 0.9154 (ptm-80) REVERT: D 840 PHE cc_start: 0.9069 (m-80) cc_final: 0.8571 (m-80) REVERT: D 854 HIS cc_start: 0.9046 (m-70) cc_final: 0.8746 (m170) REVERT: D 862 ASP cc_start: 0.9145 (t0) cc_final: 0.8912 (t0) REVERT: D 866 ARG cc_start: 0.9096 (ptt180) cc_final: 0.8618 (ptm160) REVERT: D 928 ASP cc_start: 0.8419 (m-30) cc_final: 0.8101 (m-30) REVERT: D 1060 ARG cc_start: 0.8887 (mmp-170) cc_final: 0.8663 (mmm160) REVERT: D 1112 MET cc_start: 0.8686 (tpt) cc_final: 0.8206 (tpp) REVERT: D 1133 HIS cc_start: 0.9356 (t70) cc_final: 0.9042 (t70) REVERT: D 1137 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8969 (mm-30) REVERT: D 1139 GLN cc_start: 0.9293 (tp-100) cc_final: 0.8902 (tp-100) REVERT: D 1140 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8844 (mt-10) REVERT: D 1151 ASP cc_start: 0.8655 (t0) cc_final: 0.8244 (t0) REVERT: D 1152 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8647 (ttmt) REVERT: D 1183 ARG cc_start: 0.9350 (ptp-110) cc_final: 0.8809 (ptp-170) REVERT: D 1232 VAL cc_start: 0.9557 (p) cc_final: 0.9293 (p) REVERT: D 1235 ASP cc_start: 0.9376 (t0) cc_final: 0.9103 (p0) REVERT: D 1242 SER cc_start: 0.8500 (p) cc_final: 0.8201 (m) REVERT: E 50 LYS cc_start: 0.9569 (mtpt) cc_final: 0.9289 (mtpt) REVERT: E 65 ASN cc_start: 0.8989 (t0) cc_final: 0.8699 (t0) REVERT: E 78 TYR cc_start: 0.8339 (m-10) cc_final: 0.8130 (m-10) REVERT: E 108 GLU cc_start: 0.9217 (pm20) cc_final: 0.8120 (tm-30) REVERT: F 213 ARG cc_start: 0.8680 (ppt170) cc_final: 0.8212 (ttp80) REVERT: F 258 TYR cc_start: 0.9261 (t80) cc_final: 0.8986 (t80) REVERT: F 352 ARG cc_start: 0.8719 (mtp-110) cc_final: 0.8411 (mtm180) REVERT: F 357 ARG cc_start: 0.9614 (tmt170) cc_final: 0.9378 (ttp80) REVERT: F 372 MET cc_start: 0.9583 (mmp) cc_final: 0.9362 (mmp) REVERT: F 377 ASN cc_start: 0.9666 (t0) cc_final: 0.8763 (t0) REVERT: J 84 MET cc_start: 0.9291 (mpp) cc_final: 0.8932 (mpp) REVERT: J 86 LEU cc_start: 0.9626 (tp) cc_final: 0.9337 (mt) REVERT: J 91 ILE cc_start: 0.8788 (pt) cc_final: 0.8439 (pt) REVERT: M 34 TYR cc_start: 0.9398 (m-80) cc_final: 0.8749 (m-80) REVERT: M 156 GLU cc_start: 0.9732 (tm-30) cc_final: 0.9428 (mm-30) outliers start: 2 outliers final: 0 residues processed: 884 average time/residue: 0.2036 time to fit residues: 277.9967 Evaluate side-chains 780 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 780 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 164 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 284 optimal weight: 0.0870 chunk 263 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 HIS C 920 HIS C1077 GLN D 369 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.110053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078790 restraints weight = 98287.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081200 restraints weight = 56996.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081642 restraints weight = 34526.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082295 restraints weight = 29944.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083507 restraints weight = 26369.611| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30158 Z= 0.145 Angle : 0.736 26.233 41380 Z= 0.379 Chirality : 0.053 1.950 4726 Planarity : 0.005 0.100 5007 Dihedral : 17.189 178.021 5172 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3441 helix: 0.19 (0.14), residues: 1395 sheet: -0.48 (0.27), residues: 341 loop : -0.96 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 624 TYR 0.026 0.002 TYR F 258 PHE 0.014 0.001 PHE F 317 TRP 0.051 0.002 TRP M 112 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00321 (30150) covalent geometry : angle 0.73348 (41368) hydrogen bonds : bond 0.04146 ( 1389) hydrogen bonds : angle 5.09405 ( 3855) metal coordination : bond 0.00688 ( 8) metal coordination : angle 3.29631 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 920 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8906 (ttp-170) cc_final: 0.8334 (ptm160) REVERT: A 30 PHE cc_start: 0.6828 (m-80) cc_final: 0.6577 (m-10) REVERT: A 34 LEU cc_start: 0.9397 (tp) cc_final: 0.9023 (tp) REVERT: A 38 LEU cc_start: 0.9804 (mt) cc_final: 0.9537 (mt) REVERT: A 72 ASP cc_start: 0.8873 (m-30) cc_final: 0.8505 (m-30) REVERT: A 138 LEU cc_start: 0.9375 (mp) cc_final: 0.9041 (mp) REVERT: A 151 GLN cc_start: 0.8377 (mp-120) cc_final: 0.8137 (pm20) REVERT: A 168 TYR cc_start: 0.7616 (m-10) cc_final: 0.7016 (m-80) REVERT: A 179 ASP cc_start: 0.9115 (t0) cc_final: 0.8868 (t0) REVERT: A 197 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8078 (mp0) REVERT: A 208 LEU cc_start: 0.9533 (mm) cc_final: 0.9307 (mp) REVERT: A 219 PHE cc_start: 0.8037 (m-80) cc_final: 0.7653 (m-80) REVERT: B 12 ASP cc_start: 0.9337 (t70) cc_final: 0.8940 (t0) REVERT: B 20 GLN cc_start: 0.8655 (mp10) cc_final: 0.8025 (mp10) REVERT: B 30 PHE cc_start: 0.9461 (m-80) cc_final: 0.9046 (m-80) REVERT: B 39 ARG cc_start: 0.9362 (tmm-80) cc_final: 0.8855 (ttp80) REVERT: B 42 LEU cc_start: 0.9803 (mt) cc_final: 0.9578 (mt) REVERT: B 120 ASN cc_start: 0.9470 (t0) cc_final: 0.9131 (t0) REVERT: B 151 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8679 (tm-30) REVERT: B 165 ASP cc_start: 0.9042 (m-30) cc_final: 0.8824 (m-30) REVERT: B 177 LYS cc_start: 0.8414 (mppt) cc_final: 0.8161 (mmtm) REVERT: B 213 LYS cc_start: 0.9604 (tptp) cc_final: 0.9364 (tppt) REVERT: B 217 GLU cc_start: 0.9394 (pt0) cc_final: 0.9152 (tm-30) REVERT: B 219 PHE cc_start: 0.9246 (m-80) cc_final: 0.8813 (m-80) REVERT: B 223 ARG cc_start: 0.9242 (ttt-90) cc_final: 0.9001 (tpt-90) REVERT: C 59 ASP cc_start: 0.9333 (m-30) cc_final: 0.8965 (m-30) REVERT: C 93 LEU cc_start: 0.9464 (tp) cc_final: 0.9185 (tp) REVERT: C 199 LEU cc_start: 0.9269 (pp) cc_final: 0.9002 (mt) REVERT: C 213 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7140 (mm-30) REVERT: C 239 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7821 (tppt) REVERT: C 279 ARG cc_start: 0.9551 (tmt170) cc_final: 0.9336 (ttp80) REVERT: C 306 TYR cc_start: 0.8681 (t80) cc_final: 0.8208 (t80) REVERT: C 308 LEU cc_start: 0.9439 (tp) cc_final: 0.9149 (tp) REVERT: C 376 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7638 (mtp-110) REVERT: C 386 GLN cc_start: 0.9415 (pt0) cc_final: 0.9146 (pt0) REVERT: C 404 MET cc_start: 0.9169 (tpt) cc_final: 0.8860 (tpt) REVERT: C 410 GLU cc_start: 0.8521 (tp30) cc_final: 0.8270 (tp30) REVERT: C 442 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8754 (tp40) REVERT: C 482 ARG cc_start: 0.8024 (mtt180) cc_final: 0.6862 (mtt90) REVERT: C 483 MET cc_start: 0.8160 (tpp) cc_final: 0.7650 (tpp) REVERT: C 511 PHE cc_start: 0.8961 (m-80) cc_final: 0.8159 (m-10) REVERT: C 531 LEU cc_start: 0.8803 (mt) cc_final: 0.8501 (mp) REVERT: C 543 GLN cc_start: 0.7697 (tt0) cc_final: 0.7337 (tm-30) REVERT: C 585 GLN cc_start: 0.8730 (tp-100) cc_final: 0.7869 (tp40) REVERT: C 594 ILE cc_start: 0.9033 (mt) cc_final: 0.8502 (pt) REVERT: C 601 ASP cc_start: 0.9144 (t70) cc_final: 0.8400 (p0) REVERT: C 611 MET cc_start: 0.8905 (ptt) cc_final: 0.8471 (ptt) REVERT: C 620 ARG cc_start: 0.9337 (tpm170) cc_final: 0.9013 (tpm170) REVERT: C 672 MET cc_start: 0.7422 (ppp) cc_final: 0.7095 (ppp) REVERT: C 680 HIS cc_start: 0.7800 (m90) cc_final: 0.7569 (m90) REVERT: C 720 LEU cc_start: 0.9115 (tp) cc_final: 0.8894 (tp) REVERT: C 753 GLU cc_start: 0.8481 (mp0) cc_final: 0.8108 (mp0) REVERT: C 846 LYS cc_start: 0.9334 (tptt) cc_final: 0.8852 (tppt) REVERT: C 873 VAL cc_start: 0.9153 (t) cc_final: 0.8270 (p) REVERT: C 892 LYS cc_start: 0.9205 (ptpt) cc_final: 0.8752 (ptpt) REVERT: C 907 LEU cc_start: 0.8774 (tp) cc_final: 0.8528 (tp) REVERT: C 926 MET cc_start: 0.8631 (tpp) cc_final: 0.8157 (tpp) REVERT: C 933 GLU cc_start: 0.8943 (tt0) cc_final: 0.8413 (tt0) REVERT: C 944 TRP cc_start: 0.8783 (p90) cc_final: 0.8384 (p90) REVERT: C 982 GLU cc_start: 0.8841 (pm20) cc_final: 0.7569 (tm-30) REVERT: C 1036 LEU cc_start: 0.8967 (mt) cc_final: 0.8715 (mt) REVERT: C 1039 ASP cc_start: 0.9163 (m-30) cc_final: 0.8762 (m-30) REVERT: C 1040 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7694 (mptt) REVERT: C 1051 MET cc_start: 0.9052 (tpp) cc_final: 0.8637 (mmm) REVERT: C 1071 MET cc_start: 0.7744 (pmm) cc_final: 0.6777 (pmm) REVERT: C 1073 CYS cc_start: 0.8802 (m) cc_final: 0.8546 (m) REVERT: C 1076 MET cc_start: 0.9088 (ttm) cc_final: 0.8712 (ttm) REVERT: C 1086 GLN cc_start: 0.9431 (pt0) cc_final: 0.9127 (pt0) REVERT: C 1090 THR cc_start: 0.9138 (m) cc_final: 0.8863 (p) REVERT: C 1092 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8540 (mtpp) REVERT: C 1128 LEU cc_start: 0.9391 (mt) cc_final: 0.9178 (mt) REVERT: D 29 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8896 (ptpp) REVERT: D 33 THR cc_start: 0.8572 (p) cc_final: 0.7851 (p) REVERT: D 64 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8339 (mtpt) REVERT: D 66 LYS cc_start: 0.9317 (ptpp) cc_final: 0.8999 (mmmt) REVERT: D 92 MET cc_start: 0.8624 (mmm) cc_final: 0.8093 (tpp) REVERT: D 262 GLN cc_start: 0.9566 (tt0) cc_final: 0.9102 (tm-30) REVERT: D 319 VAL cc_start: 0.9058 (t) cc_final: 0.8734 (p) REVERT: D 341 ASN cc_start: 0.9146 (m-40) cc_final: 0.8628 (m110) REVERT: D 386 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7804 (mmm160) REVERT: D 427 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.7699 (ttm-80) REVERT: D 440 GLN cc_start: 0.8982 (mt0) cc_final: 0.8434 (mt0) REVERT: D 471 SER cc_start: 0.9264 (t) cc_final: 0.8653 (p) REVERT: D 475 MET cc_start: 0.9094 (mmp) cc_final: 0.8843 (mmp) REVERT: D 503 THR cc_start: 0.8679 (p) cc_final: 0.7998 (p) REVERT: D 504 LEU cc_start: 0.9125 (tp) cc_final: 0.8811 (tp) REVERT: D 505 HIS cc_start: 0.9238 (p-80) cc_final: 0.8965 (p-80) REVERT: D 510 GLN cc_start: 0.8337 (mp10) cc_final: 0.7764 (mp10) REVERT: D 515 MET cc_start: 0.8632 (mmp) cc_final: 0.8385 (mmm) REVERT: D 523 GLN cc_start: 0.8598 (tt0) cc_final: 0.8059 (tp40) REVERT: D 524 LEU cc_start: 0.9046 (tp) cc_final: 0.8660 (tp) REVERT: D 527 LEU cc_start: 0.9185 (mt) cc_final: 0.8960 (mt) REVERT: D 532 PHE cc_start: 0.7907 (m-80) cc_final: 0.7273 (m-80) REVERT: D 574 LEU cc_start: 0.8944 (mt) cc_final: 0.8554 (mt) REVERT: D 576 MET cc_start: 0.9034 (ppp) cc_final: 0.8726 (ppp) REVERT: D 581 MET cc_start: 0.8881 (mtm) cc_final: 0.8532 (mtm) REVERT: D 641 ARG cc_start: 0.9039 (tpt-90) cc_final: 0.8743 (tpp80) REVERT: D 672 MET cc_start: 0.9302 (ttp) cc_final: 0.9005 (ttp) REVERT: D 675 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9190 (tm-30) REVERT: D 706 MET cc_start: 0.8801 (pmm) cc_final: 0.8288 (pmm) REVERT: D 717 LYS cc_start: 0.9350 (tmmt) cc_final: 0.8657 (tmmt) REVERT: D 733 MET cc_start: 0.8235 (ppp) cc_final: 0.7438 (ppp) REVERT: D 780 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8444 (tt0) REVERT: D 784 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9031 (mm-30) REVERT: D 815 ARG cc_start: 0.9470 (tmm-80) cc_final: 0.9193 (ttp80) REVERT: D 840 PHE cc_start: 0.8971 (m-80) cc_final: 0.8554 (m-80) REVERT: D 854 HIS cc_start: 0.9025 (m-70) cc_final: 0.8738 (m170) REVERT: D 866 ARG cc_start: 0.9091 (ptt180) cc_final: 0.8726 (ptm160) REVERT: D 924 THR cc_start: 0.9013 (m) cc_final: 0.8466 (p) REVERT: D 928 ASP cc_start: 0.8402 (m-30) cc_final: 0.8103 (m-30) REVERT: D 993 GLU cc_start: 0.8291 (mp0) cc_final: 0.7962 (mp0) REVERT: D 1060 ARG cc_start: 0.8859 (mmp-170) cc_final: 0.8606 (mmm160) REVERT: D 1077 TYR cc_start: 0.8118 (m-10) cc_final: 0.7857 (m-10) REVERT: D 1112 MET cc_start: 0.9025 (tpt) cc_final: 0.8806 (tpp) REVERT: D 1133 HIS cc_start: 0.9279 (t70) cc_final: 0.8961 (t70) REVERT: D 1137 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8944 (mm-30) REVERT: D 1139 GLN cc_start: 0.9252 (tp-100) cc_final: 0.8794 (tp-100) REVERT: D 1140 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8857 (mt-10) REVERT: D 1151 ASP cc_start: 0.8592 (t0) cc_final: 0.8185 (t0) REVERT: D 1183 ARG cc_start: 0.9322 (ptp-110) cc_final: 0.8808 (ptp-170) REVERT: D 1212 LYS cc_start: 0.9584 (mtmt) cc_final: 0.9348 (ptpt) REVERT: D 1229 THR cc_start: 0.9144 (m) cc_final: 0.8818 (m) REVERT: D 1235 ASP cc_start: 0.9333 (t0) cc_final: 0.9023 (p0) REVERT: D 1242 SER cc_start: 0.8459 (p) cc_final: 0.8224 (m) REVERT: E 62 ARG cc_start: 0.8938 (mtt-85) cc_final: 0.8658 (ttm-80) REVERT: E 65 ASN cc_start: 0.8992 (t0) cc_final: 0.8667 (t0) REVERT: E 107 THR cc_start: 0.8978 (p) cc_final: 0.8668 (p) REVERT: E 108 GLU cc_start: 0.9298 (pm20) cc_final: 0.8217 (tm-30) REVERT: F 213 ARG cc_start: 0.8697 (ppt170) cc_final: 0.8201 (ttp80) REVERT: F 258 TYR cc_start: 0.9332 (t80) cc_final: 0.9017 (t80) REVERT: F 333 GLU cc_start: 0.8174 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 352 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8410 (mtm180) REVERT: F 357 ARG cc_start: 0.9617 (tmt170) cc_final: 0.9338 (tmm160) REVERT: F 372 MET cc_start: 0.9521 (mmp) cc_final: 0.9175 (mmm) REVERT: J 86 LEU cc_start: 0.9622 (tp) cc_final: 0.9341 (mt) REVERT: J 91 ILE cc_start: 0.8831 (pt) cc_final: 0.8495 (pt) REVERT: M 34 TYR cc_start: 0.9366 (m-80) cc_final: 0.8695 (m-80) REVERT: M 156 GLU cc_start: 0.9739 (tm-30) cc_final: 0.9402 (mm-30) outliers start: 0 outliers final: 0 residues processed: 920 average time/residue: 0.1938 time to fit residues: 276.8620 Evaluate side-chains 787 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 787 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 268 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 153 optimal weight: 0.0670 chunk 199 optimal weight: 0.7980 chunk 216 optimal weight: 20.0000 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS B 226 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 102 ASN M 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075589 restraints weight = 102259.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076708 restraints weight = 61588.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078129 restraints weight = 35790.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078415 restraints weight = 28831.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078939 restraints weight = 25349.097| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30158 Z= 0.216 Angle : 0.767 26.754 41380 Z= 0.402 Chirality : 0.053 1.909 4726 Planarity : 0.006 0.087 5007 Dihedral : 17.304 176.698 5172 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 0.07 % Allowed : 0.94 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3441 helix: 0.08 (0.14), residues: 1417 sheet: -0.57 (0.27), residues: 358 loop : -1.12 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 353 TYR 0.024 0.002 TYR F 346 PHE 0.022 0.002 PHE D 107 TRP 0.043 0.002 TRP M 112 HIS 0.016 0.002 HIS C 920 Details of bonding type rmsd covalent geometry : bond 0.00463 (30150) covalent geometry : angle 0.76425 (41368) hydrogen bonds : bond 0.04535 ( 1389) hydrogen bonds : angle 5.29470 ( 3855) metal coordination : bond 0.01096 ( 8) metal coordination : angle 4.15218 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 865 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8861 (ttp-170) cc_final: 0.8300 (ptm160) REVERT: A 27 GLU cc_start: 0.8842 (tp30) cc_final: 0.7904 (tp30) REVERT: A 30 PHE cc_start: 0.7004 (m-80) cc_final: 0.6040 (m-80) REVERT: A 34 LEU cc_start: 0.9444 (tp) cc_final: 0.9139 (tp) REVERT: A 38 LEU cc_start: 0.9806 (mt) cc_final: 0.9548 (mt) REVERT: A 138 LEU cc_start: 0.9367 (mp) cc_final: 0.9029 (mp) REVERT: A 141 GLU cc_start: 0.8266 (tp30) cc_final: 0.7623 (tp30) REVERT: A 168 TYR cc_start: 0.7756 (m-10) cc_final: 0.7016 (m-80) REVERT: A 179 ASP cc_start: 0.9191 (t0) cc_final: 0.8880 (t0) REVERT: A 197 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8091 (mp0) REVERT: A 219 PHE cc_start: 0.8290 (m-80) cc_final: 0.7901 (m-80) REVERT: B 12 ASP cc_start: 0.9341 (t70) cc_final: 0.8801 (t0) REVERT: B 20 GLN cc_start: 0.8631 (mp10) cc_final: 0.7969 (mp10) REVERT: B 27 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 30 PHE cc_start: 0.9401 (m-80) cc_final: 0.8797 (m-80) REVERT: B 39 ARG cc_start: 0.9362 (tmm-80) cc_final: 0.8735 (ttp80) REVERT: B 42 LEU cc_start: 0.9802 (mt) cc_final: 0.9565 (mt) REVERT: B 81 LYS cc_start: 0.8913 (tppt) cc_final: 0.8712 (tptt) REVERT: B 95 MET cc_start: 0.7958 (tpt) cc_final: 0.7707 (tpp) REVERT: B 151 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8820 (tm-30) REVERT: B 177 LYS cc_start: 0.8372 (mppt) cc_final: 0.8161 (mmtm) REVERT: B 213 LYS cc_start: 0.9609 (tptp) cc_final: 0.9367 (tppt) REVERT: B 217 GLU cc_start: 0.9404 (pt0) cc_final: 0.9129 (tm-30) REVERT: B 219 PHE cc_start: 0.9338 (m-80) cc_final: 0.8956 (m-80) REVERT: B 223 ARG cc_start: 0.9315 (ttt-90) cc_final: 0.9018 (tpt-90) REVERT: C 59 ASP cc_start: 0.9411 (m-30) cc_final: 0.9019 (m-30) REVERT: C 93 LEU cc_start: 0.9456 (tp) cc_final: 0.9160 (tp) REVERT: C 213 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 239 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7945 (tppt) REVERT: C 306 TYR cc_start: 0.8737 (t80) cc_final: 0.8315 (t80) REVERT: C 308 LEU cc_start: 0.9445 (tp) cc_final: 0.9179 (tp) REVERT: C 349 HIS cc_start: 0.9129 (t-90) cc_final: 0.8887 (t-90) REVERT: C 396 MET cc_start: 0.9003 (tpt) cc_final: 0.8224 (tpt) REVERT: C 404 MET cc_start: 0.9214 (tpt) cc_final: 0.8937 (tpt) REVERT: C 410 GLU cc_start: 0.8538 (tp30) cc_final: 0.8205 (tp30) REVERT: C 483 MET cc_start: 0.8395 (tpp) cc_final: 0.7632 (tpp) REVERT: C 511 PHE cc_start: 0.9029 (m-80) cc_final: 0.8343 (m-10) REVERT: C 531 LEU cc_start: 0.8804 (mt) cc_final: 0.8520 (mt) REVERT: C 543 GLN cc_start: 0.7758 (tt0) cc_final: 0.7160 (tt0) REVERT: C 579 MET cc_start: 0.9154 (ppp) cc_final: 0.8581 (ppp) REVERT: C 585 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8091 (tp40) REVERT: C 593 MET cc_start: 0.9390 (mmt) cc_final: 0.8828 (mmp) REVERT: C 594 ILE cc_start: 0.9102 (mt) cc_final: 0.8472 (pt) REVERT: C 611 MET cc_start: 0.8873 (ptt) cc_final: 0.8463 (ptt) REVERT: C 613 ARG cc_start: 0.9220 (mtm110) cc_final: 0.8536 (mtm-85) REVERT: C 620 ARG cc_start: 0.9344 (tpm170) cc_final: 0.9015 (tpm170) REVERT: C 672 MET cc_start: 0.7632 (ppp) cc_final: 0.6437 (ppp) REVERT: C 674 LYS cc_start: 0.7947 (mmpt) cc_final: 0.7570 (mmpt) REVERT: C 680 HIS cc_start: 0.8100 (m90) cc_final: 0.7652 (m90) REVERT: C 713 MET cc_start: 0.8514 (tpp) cc_final: 0.8201 (ptp) REVERT: C 846 LYS cc_start: 0.9360 (tptt) cc_final: 0.8988 (tppt) REVERT: C 881 ASP cc_start: 0.7305 (m-30) cc_final: 0.7083 (m-30) REVERT: C 892 LYS cc_start: 0.9335 (ptpt) cc_final: 0.8977 (ptpt) REVERT: C 933 GLU cc_start: 0.8687 (tt0) cc_final: 0.8385 (tt0) REVERT: C 944 TRP cc_start: 0.8884 (p90) cc_final: 0.8257 (p90) REVERT: C 962 GLU cc_start: 0.8405 (mp0) cc_final: 0.8203 (mp0) REVERT: C 978 ASP cc_start: 0.8343 (p0) cc_final: 0.7593 (t0) REVERT: C 982 GLU cc_start: 0.8929 (pm20) cc_final: 0.7963 (pp20) REVERT: C 988 LEU cc_start: 0.9560 (mm) cc_final: 0.9245 (mm) REVERT: C 1036 LEU cc_start: 0.8939 (mt) cc_final: 0.8596 (mt) REVERT: C 1039 ASP cc_start: 0.9144 (m-30) cc_final: 0.8655 (m-30) REVERT: C 1040 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7783 (mptt) REVERT: C 1071 MET cc_start: 0.7818 (pmm) cc_final: 0.6816 (pmm) REVERT: C 1073 CYS cc_start: 0.8798 (m) cc_final: 0.8536 (m) REVERT: C 1076 MET cc_start: 0.9165 (ttm) cc_final: 0.8779 (ttm) REVERT: C 1086 GLN cc_start: 0.9417 (pt0) cc_final: 0.9182 (pt0) REVERT: C 1092 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8243 (mtpp) REVERT: C 1128 LEU cc_start: 0.9397 (mt) cc_final: 0.9179 (mt) REVERT: D 29 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8986 (ptpp) REVERT: D 66 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8896 (mmmt) REVERT: D 92 MET cc_start: 0.8556 (mmm) cc_final: 0.8009 (tpp) REVERT: D 118 LEU cc_start: 0.9419 (mm) cc_final: 0.9107 (mm) REVERT: D 119 ASP cc_start: 0.8550 (t70) cc_final: 0.8280 (t70) REVERT: D 120 LEU cc_start: 0.8885 (mm) cc_final: 0.8401 (tp) REVERT: D 131 PHE cc_start: 0.9284 (m-80) cc_final: 0.8960 (m-10) REVERT: D 262 GLN cc_start: 0.9583 (tt0) cc_final: 0.9034 (tm-30) REVERT: D 319 VAL cc_start: 0.9038 (t) cc_final: 0.8613 (t) REVERT: D 341 ASN cc_start: 0.9100 (m-40) cc_final: 0.8623 (m110) REVERT: D 350 ARG cc_start: 0.9324 (mtt180) cc_final: 0.8945 (mtp180) REVERT: D 364 GLU cc_start: 0.8865 (pp20) cc_final: 0.8576 (pp20) REVERT: D 379 ASP cc_start: 0.9510 (t0) cc_final: 0.9271 (t0) REVERT: D 386 ARG cc_start: 0.8434 (tpt170) cc_final: 0.8039 (mmm160) REVERT: D 397 ARG cc_start: 0.8882 (tmm-80) cc_final: 0.8632 (tmm-80) REVERT: D 424 TYR cc_start: 0.8806 (m-10) cc_final: 0.8516 (m-10) REVERT: D 427 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: D 440 GLN cc_start: 0.9012 (mt0) cc_final: 0.8512 (mt0) REVERT: D 471 SER cc_start: 0.9323 (t) cc_final: 0.8920 (p) REVERT: D 475 MET cc_start: 0.9094 (mmp) cc_final: 0.8833 (mmp) REVERT: D 503 THR cc_start: 0.8893 (p) cc_final: 0.8208 (p) REVERT: D 504 LEU cc_start: 0.9152 (tp) cc_final: 0.8774 (tp) REVERT: D 510 GLN cc_start: 0.8491 (mp10) cc_final: 0.8002 (mp10) REVERT: D 527 LEU cc_start: 0.9199 (mt) cc_final: 0.8878 (mt) REVERT: D 532 PHE cc_start: 0.8240 (m-80) cc_final: 0.7841 (m-80) REVERT: D 552 GLN cc_start: 0.8463 (mp10) cc_final: 0.8080 (mp10) REVERT: D 554 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8407 (mt-10) REVERT: D 574 LEU cc_start: 0.8970 (mt) cc_final: 0.8528 (mt) REVERT: D 576 MET cc_start: 0.8982 (ppp) cc_final: 0.8709 (ppp) REVERT: D 581 MET cc_start: 0.9008 (mtm) cc_final: 0.8736 (mtm) REVERT: D 641 ARG cc_start: 0.9111 (tpt-90) cc_final: 0.8773 (tpp80) REVERT: D 672 MET cc_start: 0.9398 (ttp) cc_final: 0.9113 (ttp) REVERT: D 675 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9156 (tm-30) REVERT: D 688 MET cc_start: 0.8167 (mmp) cc_final: 0.7588 (mmp) REVERT: D 698 ASN cc_start: 0.9433 (t0) cc_final: 0.9195 (t0) REVERT: D 706 MET cc_start: 0.8735 (pmm) cc_final: 0.8358 (pmm) REVERT: D 733 MET cc_start: 0.8429 (ppp) cc_final: 0.8062 (ppp) REVERT: D 780 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8496 (tt0) REVERT: D 784 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9031 (mm-30) REVERT: D 815 ARG cc_start: 0.9475 (tmm-80) cc_final: 0.9235 (ttp80) REVERT: D 820 MET cc_start: 0.8922 (tmm) cc_final: 0.8645 (tmm) REVERT: D 854 HIS cc_start: 0.9048 (m-70) cc_final: 0.8796 (m-70) REVERT: D 866 ARG cc_start: 0.9072 (ptt180) cc_final: 0.8667 (ptm160) REVERT: D 928 ASP cc_start: 0.8355 (m-30) cc_final: 0.8063 (m-30) REVERT: D 993 GLU cc_start: 0.8371 (mp0) cc_final: 0.7996 (mp0) REVERT: D 1060 ARG cc_start: 0.8914 (mmp-170) cc_final: 0.8674 (mmm160) REVERT: D 1133 HIS cc_start: 0.9307 (t70) cc_final: 0.9013 (t70) REVERT: D 1137 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8968 (mm-30) REVERT: D 1139 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8864 (tp-100) REVERT: D 1140 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8831 (mt-10) REVERT: D 1151 ASP cc_start: 0.8677 (t0) cc_final: 0.8332 (t0) REVERT: D 1183 ARG cc_start: 0.9282 (ptp-110) cc_final: 0.8920 (ptp-170) REVERT: D 1231 ARG cc_start: 0.9021 (ptt90) cc_final: 0.8816 (ptt90) REVERT: E 65 ASN cc_start: 0.9044 (t0) cc_final: 0.8759 (t0) REVERT: E 78 TYR cc_start: 0.8528 (m-10) cc_final: 0.8245 (m-10) REVERT: E 107 THR cc_start: 0.9000 (p) cc_final: 0.8695 (p) REVERT: E 108 GLU cc_start: 0.9294 (pm20) cc_final: 0.8196 (tm-30) REVERT: F 213 ARG cc_start: 0.8715 (ppt170) cc_final: 0.8166 (ttp80) REVERT: F 258 TYR cc_start: 0.9343 (t80) cc_final: 0.9016 (t80) REVERT: F 263 MET cc_start: 0.8753 (mmp) cc_final: 0.8527 (mmm) REVERT: F 352 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.8436 (mtm180) REVERT: F 357 ARG cc_start: 0.9595 (tmt170) cc_final: 0.9332 (ttp80) REVERT: F 359 MET cc_start: 0.9327 (mmp) cc_final: 0.9121 (mmm) REVERT: F 372 MET cc_start: 0.9541 (mmp) cc_final: 0.9188 (mmm) REVERT: F 485 GLN cc_start: 0.9531 (pm20) cc_final: 0.9284 (pm20) REVERT: J 86 LEU cc_start: 0.9632 (tp) cc_final: 0.9350 (mt) REVERT: J 91 ILE cc_start: 0.8875 (pt) cc_final: 0.8531 (pt) REVERT: M 34 TYR cc_start: 0.9396 (m-80) cc_final: 0.8701 (m-80) REVERT: M 156 GLU cc_start: 0.9750 (tm-30) cc_final: 0.9395 (mm-30) outliers start: 2 outliers final: 0 residues processed: 866 average time/residue: 0.2079 time to fit residues: 279.5290 Evaluate side-chains 743 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 203 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN D1001 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.107888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077011 restraints weight = 101793.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078602 restraints weight = 60456.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079255 restraints weight = 36646.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080269 restraints weight = 31038.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080325 restraints weight = 27032.779| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30158 Z= 0.167 Angle : 0.762 26.773 41380 Z= 0.395 Chirality : 0.053 1.936 4726 Planarity : 0.005 0.085 5007 Dihedral : 17.283 176.651 5172 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3441 helix: 0.06 (0.14), residues: 1404 sheet: -0.57 (0.27), residues: 342 loop : -1.09 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 173 TYR 0.020 0.002 TYR F 258 PHE 0.019 0.002 PHE C1121 TRP 0.043 0.002 TRP M 112 HIS 0.008 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00368 (30150) covalent geometry : angle 0.75796 (41368) hydrogen bonds : bond 0.04271 ( 1389) hydrogen bonds : angle 5.24274 ( 3855) metal coordination : bond 0.01234 ( 8) metal coordination : angle 4.60743 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 893 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8842 (ttp-170) cc_final: 0.8219 (ptm160) REVERT: A 27 GLU cc_start: 0.8825 (tp30) cc_final: 0.7836 (tp30) REVERT: A 30 PHE cc_start: 0.6912 (m-80) cc_final: 0.6152 (m-80) REVERT: A 34 LEU cc_start: 0.9387 (tp) cc_final: 0.9075 (tp) REVERT: A 38 LEU cc_start: 0.9791 (mt) cc_final: 0.9523 (mt) REVERT: A 83 LEU cc_start: 0.9722 (tp) cc_final: 0.9337 (tp) REVERT: A 123 MET cc_start: 0.8220 (ptm) cc_final: 0.7982 (ppp) REVERT: A 138 LEU cc_start: 0.9395 (mp) cc_final: 0.9099 (mp) REVERT: A 168 TYR cc_start: 0.7814 (m-10) cc_final: 0.7171 (m-80) REVERT: A 179 ASP cc_start: 0.9193 (t0) cc_final: 0.8931 (t0) REVERT: A 197 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8232 (mp0) REVERT: A 219 PHE cc_start: 0.8223 (m-80) cc_final: 0.7877 (m-80) REVERT: B 9 LEU cc_start: 0.7917 (pp) cc_final: 0.7704 (tt) REVERT: B 12 ASP cc_start: 0.9328 (t70) cc_final: 0.8806 (t0) REVERT: B 20 GLN cc_start: 0.8684 (mp10) cc_final: 0.8142 (mp10) REVERT: B 27 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8442 (tm-30) REVERT: B 30 PHE cc_start: 0.9384 (m-80) cc_final: 0.8772 (m-80) REVERT: B 39 ARG cc_start: 0.9304 (tmm-80) cc_final: 0.8757 (ttp80) REVERT: B 42 LEU cc_start: 0.9785 (mt) cc_final: 0.9533 (mt) REVERT: B 95 MET cc_start: 0.8284 (tpt) cc_final: 0.8028 (tpp) REVERT: B 151 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8850 (tm-30) REVERT: B 177 LYS cc_start: 0.8456 (mppt) cc_final: 0.8201 (mmtm) REVERT: B 213 LYS cc_start: 0.9599 (tptp) cc_final: 0.9364 (tppt) REVERT: B 217 GLU cc_start: 0.9408 (pt0) cc_final: 0.9164 (tm-30) REVERT: B 219 PHE cc_start: 0.9294 (m-80) cc_final: 0.8931 (m-80) REVERT: B 223 ARG cc_start: 0.9302 (ttt-90) cc_final: 0.9031 (tpt-90) REVERT: C 59 ASP cc_start: 0.9374 (m-30) cc_final: 0.8992 (m-30) REVERT: C 93 LEU cc_start: 0.9445 (tp) cc_final: 0.9158 (tp) REVERT: C 213 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 239 LYS cc_start: 0.8310 (mmtp) cc_final: 0.8031 (tppt) REVERT: C 300 PHE cc_start: 0.8821 (m-80) cc_final: 0.7370 (m-80) REVERT: C 306 TYR cc_start: 0.8498 (t80) cc_final: 0.7766 (t80) REVERT: C 308 LEU cc_start: 0.9438 (tp) cc_final: 0.9160 (tp) REVERT: C 349 HIS cc_start: 0.9045 (t-90) cc_final: 0.8780 (t-90) REVERT: C 355 MET cc_start: 0.8501 (tmm) cc_final: 0.8241 (ttp) REVERT: C 376 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7465 (mtp85) REVERT: C 386 GLN cc_start: 0.9426 (pt0) cc_final: 0.9146 (pt0) REVERT: C 396 MET cc_start: 0.8994 (tpt) cc_final: 0.8148 (tpt) REVERT: C 410 GLU cc_start: 0.8559 (tp30) cc_final: 0.8344 (tp30) REVERT: C 483 MET cc_start: 0.8322 (tpp) cc_final: 0.7780 (tpp) REVERT: C 511 PHE cc_start: 0.8944 (m-80) cc_final: 0.8294 (m-10) REVERT: C 527 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8974 (mm-30) REVERT: C 543 GLN cc_start: 0.7551 (tt0) cc_final: 0.7326 (tm-30) REVERT: C 579 MET cc_start: 0.9170 (ppp) cc_final: 0.8637 (ppp) REVERT: C 585 GLN cc_start: 0.8705 (tp-100) cc_final: 0.7909 (tp40) REVERT: C 593 MET cc_start: 0.9415 (mmt) cc_final: 0.8850 (mmp) REVERT: C 611 MET cc_start: 0.8837 (ptt) cc_final: 0.8453 (ptt) REVERT: C 620 ARG cc_start: 0.9326 (tpm170) cc_final: 0.9020 (tpm170) REVERT: C 672 MET cc_start: 0.7726 (ppp) cc_final: 0.6481 (ppp) REVERT: C 674 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7543 (mmpt) REVERT: C 680 HIS cc_start: 0.7752 (m90) cc_final: 0.7514 (m90) REVERT: C 713 MET cc_start: 0.8461 (tpp) cc_final: 0.8148 (ptp) REVERT: C 753 GLU cc_start: 0.8232 (mp0) cc_final: 0.7966 (mp0) REVERT: C 846 LYS cc_start: 0.9359 (tptt) cc_final: 0.8926 (tppt) REVERT: C 892 LYS cc_start: 0.9228 (ptpt) cc_final: 0.8817 (ptpt) REVERT: C 930 GLN cc_start: 0.9373 (pt0) cc_final: 0.9169 (pt0) REVERT: C 933 GLU cc_start: 0.8720 (tt0) cc_final: 0.8213 (tt0) REVERT: C 939 CYS cc_start: 0.9429 (m) cc_final: 0.9201 (m) REVERT: C 944 TRP cc_start: 0.8891 (p90) cc_final: 0.8283 (p90) REVERT: C 962 GLU cc_start: 0.8400 (mp0) cc_final: 0.8182 (mp0) REVERT: C 978 ASP cc_start: 0.8299 (p0) cc_final: 0.7897 (p0) REVERT: C 982 GLU cc_start: 0.8937 (pm20) cc_final: 0.8205 (pp20) REVERT: C 988 LEU cc_start: 0.9567 (mm) cc_final: 0.9276 (mm) REVERT: C 1036 LEU cc_start: 0.8989 (mt) cc_final: 0.8580 (mt) REVERT: C 1039 ASP cc_start: 0.9163 (m-30) cc_final: 0.8741 (m-30) REVERT: C 1040 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7710 (mptt) REVERT: C 1071 MET cc_start: 0.7861 (pmm) cc_final: 0.6946 (pmm) REVERT: C 1076 MET cc_start: 0.9390 (ttm) cc_final: 0.9018 (ttm) REVERT: C 1086 GLN cc_start: 0.9402 (pt0) cc_final: 0.9145 (pt0) REVERT: C 1092 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8480 (mtpp) REVERT: C 1108 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9099 (mtmm) REVERT: C 1128 LEU cc_start: 0.9395 (mt) cc_final: 0.9170 (mt) REVERT: D 29 LYS cc_start: 0.9230 (ptpp) cc_final: 0.8903 (ptpp) REVERT: D 66 LYS cc_start: 0.9233 (ptpp) cc_final: 0.8920 (mmmt) REVERT: D 77 ARG cc_start: 0.9678 (mmm-85) cc_final: 0.9339 (mmm-85) REVERT: D 92 MET cc_start: 0.8629 (mmm) cc_final: 0.8030 (tpp) REVERT: D 118 LEU cc_start: 0.9410 (mm) cc_final: 0.9082 (mm) REVERT: D 119 ASP cc_start: 0.8497 (t70) cc_final: 0.8216 (t70) REVERT: D 120 LEU cc_start: 0.8923 (mm) cc_final: 0.8372 (tp) REVERT: D 131 PHE cc_start: 0.9268 (m-80) cc_final: 0.8934 (m-10) REVERT: D 147 GLU cc_start: 0.9464 (tp30) cc_final: 0.9145 (tm-30) REVERT: D 262 GLN cc_start: 0.9564 (tt0) cc_final: 0.9092 (tm-30) REVERT: D 319 VAL cc_start: 0.9049 (t) cc_final: 0.8609 (t) REVERT: D 341 ASN cc_start: 0.9141 (m-40) cc_final: 0.8662 (m110) REVERT: D 345 ARG cc_start: 0.9171 (ttm170) cc_final: 0.8880 (ttt180) REVERT: D 350 ARG cc_start: 0.9240 (mtt180) cc_final: 0.8974 (mtp180) REVERT: D 364 GLU cc_start: 0.8877 (pp20) cc_final: 0.8544 (pp20) REVERT: D 397 ARG cc_start: 0.8840 (tmm-80) cc_final: 0.8556 (tmm-80) REVERT: D 424 TYR cc_start: 0.8739 (m-10) cc_final: 0.8383 (m-10) REVERT: D 427 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: D 436 LEU cc_start: 0.8919 (mm) cc_final: 0.8000 (tp) REVERT: D 440 GLN cc_start: 0.9048 (mt0) cc_final: 0.8222 (mt0) REVERT: D 471 SER cc_start: 0.9307 (t) cc_final: 0.8760 (p) REVERT: D 475 MET cc_start: 0.9084 (mmp) cc_final: 0.8839 (mmp) REVERT: D 503 THR cc_start: 0.8673 (p) cc_final: 0.8156 (p) REVERT: D 504 LEU cc_start: 0.9041 (tp) cc_final: 0.8680 (tp) REVERT: D 510 GLN cc_start: 0.8480 (mp10) cc_final: 0.7992 (mp10) REVERT: D 515 MET cc_start: 0.8101 (mmm) cc_final: 0.7839 (mmm) REVERT: D 523 GLN cc_start: 0.8680 (tt0) cc_final: 0.8026 (tp-100) REVERT: D 524 LEU cc_start: 0.9116 (tp) cc_final: 0.8395 (tp) REVERT: D 532 PHE cc_start: 0.8260 (m-80) cc_final: 0.7852 (m-80) REVERT: D 552 GLN cc_start: 0.8440 (mp10) cc_final: 0.8095 (mp10) REVERT: D 556 ARG cc_start: 0.9094 (tpt170) cc_final: 0.8658 (tpt-90) REVERT: D 574 LEU cc_start: 0.8963 (mt) cc_final: 0.8538 (mt) REVERT: D 576 MET cc_start: 0.9021 (ppp) cc_final: 0.8747 (ppp) REVERT: D 581 MET cc_start: 0.8878 (mtm) cc_final: 0.8614 (mtm) REVERT: D 633 ILE cc_start: 0.9515 (pt) cc_final: 0.9015 (mm) REVERT: D 640 LEU cc_start: 0.9047 (mp) cc_final: 0.7911 (tt) REVERT: D 667 THR cc_start: 0.9276 (p) cc_final: 0.9052 (t) REVERT: D 672 MET cc_start: 0.9363 (ttp) cc_final: 0.9032 (ttp) REVERT: D 675 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9132 (tm-30) REVERT: D 698 ASN cc_start: 0.9410 (t0) cc_final: 0.9205 (t0) REVERT: D 706 MET cc_start: 0.8790 (pmm) cc_final: 0.8356 (pmm) REVERT: D 717 LYS cc_start: 0.9442 (tmmt) cc_final: 0.9021 (tmmt) REVERT: D 780 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8496 (tt0) REVERT: D 784 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9026 (mm-30) REVERT: D 815 ARG cc_start: 0.9478 (tmm-80) cc_final: 0.9175 (ttp80) REVERT: D 840 PHE cc_start: 0.8950 (m-80) cc_final: 0.8611 (m-80) REVERT: D 854 HIS cc_start: 0.9013 (m-70) cc_final: 0.8803 (m-70) REVERT: D 866 ARG cc_start: 0.9054 (ptt180) cc_final: 0.8612 (ptm160) REVERT: D 924 THR cc_start: 0.9068 (m) cc_final: 0.8519 (p) REVERT: D 928 ASP cc_start: 0.8348 (m-30) cc_final: 0.8049 (m-30) REVERT: D 993 GLU cc_start: 0.8332 (mp0) cc_final: 0.7996 (mp0) REVERT: D 1012 MET cc_start: 0.7261 (mmt) cc_final: 0.7037 (mmm) REVERT: D 1033 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8643 (tp30) REVERT: D 1060 ARG cc_start: 0.8862 (mmp-170) cc_final: 0.8613 (mmm160) REVERT: D 1133 HIS cc_start: 0.9253 (t70) cc_final: 0.8925 (t70) REVERT: D 1137 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8927 (mm-30) REVERT: D 1139 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8773 (tp-100) REVERT: D 1140 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8838 (mt-10) REVERT: D 1151 ASP cc_start: 0.8568 (t0) cc_final: 0.8207 (t0) REVERT: D 1183 ARG cc_start: 0.9286 (ptp-110) cc_final: 0.8833 (ptp-170) REVERT: D 1208 MET cc_start: 0.7861 (mpp) cc_final: 0.7592 (mpp) REVERT: D 1244 LYS cc_start: 0.9480 (mmtm) cc_final: 0.8920 (tppt) REVERT: E 46 ARG cc_start: 0.9118 (mpt90) cc_final: 0.8715 (mtt90) REVERT: E 65 ASN cc_start: 0.9034 (t0) cc_final: 0.8721 (t0) REVERT: E 78 TYR cc_start: 0.8542 (m-10) cc_final: 0.8289 (m-10) REVERT: E 107 THR cc_start: 0.8961 (p) cc_final: 0.8641 (p) REVERT: E 108 GLU cc_start: 0.9253 (pm20) cc_final: 0.8200 (tm-30) REVERT: F 213 ARG cc_start: 0.8710 (ppt170) cc_final: 0.8208 (ttp80) REVERT: F 258 TYR cc_start: 0.9311 (t80) cc_final: 0.9002 (t80) REVERT: F 352 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8409 (mtm180) REVERT: F 357 ARG cc_start: 0.9568 (tmt170) cc_final: 0.9276 (ttp80) REVERT: F 372 MET cc_start: 0.9496 (mmp) cc_final: 0.9268 (mmp) REVERT: F 485 GLN cc_start: 0.9433 (pm20) cc_final: 0.9163 (pm20) REVERT: J 86 LEU cc_start: 0.9633 (tp) cc_final: 0.9352 (mt) REVERT: J 91 ILE cc_start: 0.8840 (pt) cc_final: 0.8528 (pt) REVERT: M 7 ASP cc_start: 0.8733 (t70) cc_final: 0.8422 (t0) REVERT: M 34 TYR cc_start: 0.9341 (m-80) cc_final: 0.8604 (m-80) REVERT: M 100 ASP cc_start: 0.9034 (t0) cc_final: 0.8747 (t0) REVERT: M 156 GLU cc_start: 0.9752 (tm-30) cc_final: 0.9395 (mm-30) outliers start: 2 outliers final: 1 residues processed: 894 average time/residue: 0.2105 time to fit residues: 290.1246 Evaluate side-chains 748 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 747 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 129 optimal weight: 0.0980 chunk 332 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 308 optimal weight: 0.9990 chunk 323 optimal weight: 20.0000 chunk 283 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1077 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS E 100 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN F 294 HIS ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.108797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077929 restraints weight = 100203.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079801 restraints weight = 58067.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081349 restraints weight = 36068.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081550 restraints weight = 28483.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081980 restraints weight = 24819.763| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30158 Z= 0.152 Angle : 0.761 26.668 41380 Z= 0.394 Chirality : 0.054 1.944 4726 Planarity : 0.005 0.086 5007 Dihedral : 17.217 175.901 5172 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3441 helix: -0.03 (0.14), residues: 1411 sheet: -0.58 (0.28), residues: 338 loop : -1.07 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 18 TYR 0.017 0.001 TYR F 258 PHE 0.024 0.002 PHE D 107 TRP 0.042 0.002 TRP M 112 HIS 0.014 0.001 HIS F 294 Details of bonding type rmsd covalent geometry : bond 0.00338 (30150) covalent geometry : angle 0.75727 (41368) hydrogen bonds : bond 0.04229 ( 1389) hydrogen bonds : angle 5.17365 ( 3855) metal coordination : bond 0.00975 ( 8) metal coordination : angle 4.47067 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.83 seconds wall clock time: 120 minutes 5.14 seconds (7205.14 seconds total)