Starting phenix.real_space_refine on Tue May 27 06:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3m_18873/05_2025/8r3m_18873.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 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 51 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 18227 2.51 5 N 5251 2.21 5 O 5789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29417 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1808 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 222} Chain: "C" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8594 Classifications: {'peptide': 1109} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1049} Chain: "D" Number of atoms: 9998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9998 Classifications: {'peptide': 1280} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1222} Chain: "E" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 656 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 77} Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2423 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "O" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "P" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 443 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2299 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 250 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 19165 SG CYS D 890 33.517 61.909 69.941 1.00 19.64 S ATOM 19727 SG CYS D 967 36.585 64.059 70.628 1.00 22.71 S ATOM 19769 SG CYS D 974 34.290 62.958 73.429 1.00 19.71 S ATOM 19788 SG CYS D 977 36.503 60.525 71.911 1.00 23.00 S ATOM 12592 SG CYS D 60 36.427 127.064 87.154 1.00 43.58 S ATOM 12610 SG CYS D 62 37.225 130.683 86.551 1.00 52.27 S ATOM 12719 SG CYS D 75 34.499 129.133 84.440 1.00 49.83 S ATOM 12745 SG CYS D 78 38.143 128.586 83.987 1.00 46.53 S Time building chain proxies: 16.66, per 1000 atoms: 0.57 Number of scatterers: 29417 At special positions: 0 Unit cell: (128.374, 170.054, 165.053, 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 96 16.00 P 51 15.00 Mg 1 11.99 O 5789 8.00 N 5251 7.00 C 18227 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: 7.84 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 44.4% alpha, 15.2% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 10.63 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.755A pdb=" N GLY 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 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.357A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.921A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.586A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) 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 224 removed outlier: 3.770A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.581A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.616A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 225 through 233 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.623A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.651A pdb=" N PHE C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 Processing helix chain 'C' and resid 325 through 342 removed outlier: 3.735A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 398 removed outlier: 3.529A pdb=" N GLN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.532A pdb=" N SER C 425 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.518A pdb=" N ARG C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 573 through 577 removed outlier: 4.504A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 603 Processing helix chain 'C' and resid 604 through 606 No H-bonds generated for 'chain 'C' and resid 604 through 606' Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.518A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 806 through 817 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 911 through 917 removed outlier: 4.250A pdb=" N ARG C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 916 " --> pdb=" O GLY C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 945 through 950 removed outlier: 4.132A pdb=" N LYS C 949 " --> pdb=" O TRP C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 981 removed outlier: 3.613A pdb=" N GLY C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1030 removed outlier: 3.509A pdb=" N ASP C1030 " --> pdb=" O LEU C1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1027 through 1030' Processing helix chain 'C' and resid 1061 through 1071 Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 3.832A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C1092 " --> pdb=" O VAL C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1122 removed outlier: 3.656A pdb=" N LEU C1115 " --> pdb=" O SER C1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.500A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.540A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 185 removed outlier: 3.641A pdb=" N GLU D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.267A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 4.010A pdb=" N ASN D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.015A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.529A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 358 removed outlier: 3.883A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 445 through 463 Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.311A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 652 removed outlier: 3.542A pdb=" N GLU D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.729A pdb=" N LEU D 675 " --> pdb=" O MET D 671 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 676 " --> pdb=" O PHE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.912A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.690A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 Processing helix chain 'D' and resid 844 through 880 removed outlier: 3.888A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA D 867 " --> pdb=" O ALA D 863 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER D 869 " --> pdb=" O ARG D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 3.565A pdb=" N VAL D1131 " --> pdb=" O GLY D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 3.952A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1193 Processing helix chain 'D' and resid 1209 through 1217 removed outlier: 4.163A pdb=" N LYS D1213 " --> pdb=" O MET D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 3.919A pdb=" N SER D1226 " --> pdb=" O LEU D1222 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1249 through 1256 removed outlier: 3.747A pdb=" N ILE D1254 " --> pdb=" O LYS D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.562A pdb=" N ASN D1270 " --> pdb=" O SER D1266 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1283 Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.604A pdb=" N THR E 33 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 34' Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.674A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 208 removed outlier: 3.582A pdb=" N LYS F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 237 removed outlier: 3.631A pdb=" N ARG F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 273 Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.858A pdb=" N TYR F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 384 through 405 removed outlier: 3.751A pdb=" N ASP F 396 " --> pdb=" O THR F 392 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 403 " --> pdb=" O GLN F 399 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F 405 " --> pdb=" O VAL F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 418 removed outlier: 3.674A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 437 through 454 removed outlier: 3.553A pdb=" N ILE F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 454 " --> pdb=" O SER F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 removed outlier: 5.438A pdb=" N VAL F 460 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 86 Processing helix chain 'J' and resid 90 through 108 Processing helix chain 'H' and resid 5 through 42 removed outlier: 3.583A pdb=" N HIS H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 66 removed outlier: 3.788A pdb=" N ALA H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.807A pdb=" N ASP H 96 " --> pdb=" O ARG H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 106 through 109 Processing helix chain 'H' and resid 110 through 115 removed outlier: 3.532A pdb=" N VAL H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 296 removed outlier: 3.634A pdb=" N ARG H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 removed outlier: 3.918A pdb=" N GLY H 331 " --> pdb=" O ALA H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 358 removed outlier: 4.870A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 358 " --> pdb=" O VAL H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 384 removed outlier: 3.532A pdb=" N ASP H 383 " --> pdb=" O GLY H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 394 removed outlier: 3.696A pdb=" N LEU H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 410 Processing helix chain 'H' and resid 437 through 447 removed outlier: 4.008A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 474 removed outlier: 3.608A pdb=" N GLY H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.994A pdb=" N PHE H 502 " --> pdb=" O LEU H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.539A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 183 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 189 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.495A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.570A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 6.373A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.394A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 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 30 through 31 removed outlier: 6.802A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.545A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 126 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N PHE C 144 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 128 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR C 142 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE C 130 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER C 140 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN C 132 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 138 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.554A pdb=" N SER C 168 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.098A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 204 " --> pdb=" O ARG C 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 514 through 515 removed outlier: 7.509A pdb=" N ALA C 533 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.751A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 7.011A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 668 Processing sheet with id=AC4, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC5, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.087A pdb=" N ILE C 726 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 888 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 756 through 757 removed outlier: 6.443A pdb=" N ASP C 752 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 856 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.889A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 797 through 799 Processing sheet with id=AC9, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD1, first strand: chain 'C' and resid 1032 through 1034 removed outlier: 3.580A pdb=" N ARG D 427 " --> pdb=" O HIS C1033 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1057 through 1060 removed outlier: 3.963A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 420 " --> pdb=" O PHE C1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1127 through 1129 removed outlier: 3.541A pdb=" N GLU D 9 " --> pdb=" O LEU C1129 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.276A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.593A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.131A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 359 through 360 removed outlier: 6.526A pdb=" N PHE D 335 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD9, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AE1, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE2, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE3, first strand: chain 'D' and resid 1076 through 1078 removed outlier: 3.603A pdb=" N VAL D1106 " --> pdb=" O GLY D1052 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1089 through 1090 removed outlier: 4.068A pdb=" N GLY D1098 " --> pdb=" O ILE D1090 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1183 Processing sheet with id=AE6, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE8, first strand: chain 'H' and resid 90 through 91 removed outlier: 7.777A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE H 72 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG H 74 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG H 125 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU H 132 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 304 through 305 1314 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 13.42 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9747 1.34 - 1.45: 3417 1.45 - 1.57: 16556 1.57 - 1.69: 102 1.69 - 1.81: 171 Bond restraints: 29993 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N ASP D 605 " pdb=" CA ASP D 605 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 1.99e+00 bond pdb=" C3' DA P 7 " pdb=" O3' DA P 7 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG PRO D 111 " pdb=" CD PRO D 111 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.16e+00 ... (remaining 29988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 39751 1.24 - 2.49: 831 2.49 - 3.73: 226 3.73 - 4.98: 33 4.98 - 6.22: 5 Bond angle restraints: 40846 Sorted by residual: angle pdb=" N GLY C 365 " pdb=" CA GLY C 365 " pdb=" C GLY C 365 " ideal model delta sigma weight residual 114.67 109.32 5.35 1.10e+00 8.26e-01 2.37e+01 angle pdb=" N ILE C 693 " pdb=" CA ILE C 693 " pdb=" C ILE C 693 " ideal model delta sigma weight residual 113.42 109.39 4.03 1.17e+00 7.31e-01 1.19e+01 angle pdb=" N ILE B 234 " pdb=" CA ILE B 234 " pdb=" C ILE B 234 " ideal model delta sigma weight residual 112.96 109.61 3.35 1.00e+00 1.00e+00 1.12e+01 angle pdb=" N GLU F 186 " pdb=" CA GLU F 186 " pdb=" CB GLU F 186 " ideal model delta sigma weight residual 110.39 115.88 -5.49 1.66e+00 3.63e-01 1.09e+01 angle pdb=" N ALA D 17 " pdb=" CA ALA D 17 " pdb=" CB ALA D 17 " ideal model delta sigma weight residual 114.17 110.73 3.44 1.14e+00 7.69e-01 9.12e+00 ... (remaining 40841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 17580 32.17 - 64.35: 619 64.35 - 96.52: 62 96.52 - 128.69: 0 128.69 - 160.87: 1 Dihedral angle restraints: 18262 sinusoidal: 7704 harmonic: 10558 Sorted by residual: dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N PHE D 413 " pdb=" CA PHE D 413 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C4' DA P 7 " pdb=" C3' DA P 7 " pdb=" O3' DA P 7 " pdb=" P DA P 8 " ideal model delta sinusoidal sigma weight residual 220.00 59.13 160.87 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA ARG D 325 " pdb=" C ARG D 325 " pdb=" N PRO D 326 " pdb=" CA PRO D 326 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2965 0.028 - 0.055: 1032 0.055 - 0.083: 318 0.083 - 0.111: 252 0.111 - 0.138: 87 Chirality restraints: 4654 Sorted by residual: chirality pdb=" CA ILE C 585 " pdb=" N ILE C 585 " pdb=" C ILE C 585 " pdb=" CB ILE C 585 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 162 " pdb=" N ILE B 162 " pdb=" C ILE B 162 " pdb=" CB ILE B 162 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE C 196 " pdb=" N ILE C 196 " pdb=" C ILE C 196 " pdb=" CB ILE C 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 4651 not shown) Planarity restraints: 5226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 148 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO C 149 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 874 " -0.233 9.50e-02 1.11e+02 1.05e-01 8.27e+00 pdb=" NE ARG D 874 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 874 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 874 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 874 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D1029 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D1030 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D1030 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D1030 " 0.027 5.00e-02 4.00e+02 ... (remaining 5223 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 147 2.54 - 3.13: 22976 3.13 - 3.72: 44343 3.72 - 4.31: 60576 4.31 - 4.90: 103516 Nonbonded interactions: 231558 Sorted by model distance: nonbonded pdb=" OE1 GLU C1118 " pdb=" NH2 ARG D 412 " model vdw 1.955 3.120 nonbonded pdb=" OD1 ASP D 383 " pdb=" OG SER D 403 " model vdw 1.972 3.040 nonbonded pdb=" OG SER D1223 " pdb=" OE1 GLU D1251 " model vdw 2.028 3.040 nonbonded pdb=" O ILE D 320 " pdb=" NH1 ARG D 325 " model vdw 2.087 3.120 nonbonded pdb=" OD2 ASP C 183 " pdb=" OG SER C 185 " model vdw 2.094 3.040 ... (remaining 231553 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' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 78.570 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.003 0.110 30001 Z= 0.112 Angle : 0.493 8.595 40858 Z= 0.275 Chirality : 0.040 0.138 4654 Planarity : 0.004 0.105 5226 Dihedral : 15.531 160.867 11460 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3662 helix: 2.16 (0.14), residues: 1405 sheet: 0.19 (0.25), residues: 410 loop : -0.15 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 104 HIS 0.007 0.001 HIS C 340 PHE 0.020 0.001 PHE C 364 TYR 0.022 0.001 TYR H 466 ARG 0.022 0.000 ARG D 874 Details of bonding type rmsd hydrogen bonds : bond 0.16177 ( 1360) hydrogen bonds : angle 5.97579 ( 3830) metal coordination : bond 0.06298 ( 8) metal coordination : angle 3.47491 ( 12) covalent geometry : bond 0.00228 (29993) covalent geometry : angle 0.48962 (40846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 3.170 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 outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.4926 time to fit residues: 272.4251 Evaluate side-chains 202 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN D 375 GLN E 85 GLN F 423 GLN H 486 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.077564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057703 restraints weight = 92824.485| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.25 r_work: 0.2897 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30001 Z= 0.142 Angle : 0.572 10.233 40858 Z= 0.301 Chirality : 0.042 0.166 4654 Planarity : 0.004 0.060 5226 Dihedral : 12.165 162.359 4624 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.81 % Allowed : 6.72 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3662 helix: 2.09 (0.14), residues: 1439 sheet: 0.33 (0.25), residues: 407 loop : -0.20 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 104 HIS 0.006 0.001 HIS C 340 PHE 0.013 0.001 PHE H 97 TYR 0.019 0.001 TYR E 53 ARG 0.007 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 1360) hydrogen bonds : angle 4.50837 ( 3830) metal coordination : bond 0.00616 ( 8) metal coordination : angle 3.74687 ( 12) covalent geometry : bond 0.00324 (29993) covalent geometry : angle 0.56871 (40846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 3.534 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: C 94 MET cc_start: 0.8676 (mtp) cc_final: 0.8042 (ptp) REVERT: C 203 LEU cc_start: 0.8396 (tp) cc_final: 0.8127 (mt) REVERT: D 74 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8800 (tp) REVERT: D 203 ARG cc_start: 0.8184 (mmp80) cc_final: 0.7957 (mmp80) REVERT: D 457 MET cc_start: 0.9085 (mtm) cc_final: 0.8885 (mtm) REVERT: D 1011 MET cc_start: 0.8279 (mtp) cc_final: 0.8051 (mtp) REVERT: D 1113 MET cc_start: 0.8616 (mmm) cc_final: 0.7938 (mmm) REVERT: J 32 TYR cc_start: 0.8623 (m-80) cc_final: 0.8347 (m-80) REVERT: H 128 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7621 (tm-30) REVERT: H 485 ASP cc_start: 0.7792 (t0) cc_final: 0.7553 (t0) outliers start: 24 outliers final: 13 residues processed: 247 average time/residue: 0.4297 time to fit residues: 169.4993 Evaluate side-chains 201 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 402 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 362 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS D 5 ASN D 245 GLN D 881 GLN F 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.053769 restraints weight = 94569.052| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.10 r_work: 0.2802 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30001 Z= 0.251 Angle : 0.618 10.779 40858 Z= 0.325 Chirality : 0.044 0.172 4654 Planarity : 0.005 0.053 5226 Dihedral : 12.478 161.360 4624 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.38 % Allowed : 8.87 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3662 helix: 1.88 (0.14), residues: 1432 sheet: 0.27 (0.25), residues: 411 loop : -0.34 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 104 HIS 0.006 0.001 HIS D 103 PHE 0.019 0.002 PHE H 97 TYR 0.020 0.002 TYR F 434 ARG 0.009 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1360) hydrogen bonds : angle 4.52078 ( 3830) metal coordination : bond 0.01260 ( 8) metal coordination : angle 4.17863 ( 12) covalent geometry : bond 0.00591 (29993) covalent geometry : angle 0.61395 (40846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9018 (tmm) cc_final: 0.8784 (tmm) REVERT: C 79 GLU cc_start: 0.8397 (tt0) cc_final: 0.8196 (tm-30) REVERT: C 145 MET cc_start: 0.8936 (mmm) cc_final: 0.8677 (mmm) REVERT: C 203 LEU cc_start: 0.8392 (tp) cc_final: 0.8104 (mt) REVERT: C 461 LEU cc_start: 0.8688 (mp) cc_final: 0.8087 (tp) REVERT: D 74 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8924 (tp) REVERT: D 92 MET cc_start: 0.9181 (mtp) cc_final: 0.8957 (mtm) REVERT: D 205 MET cc_start: 0.5367 (tpp) cc_final: 0.4815 (tpp) REVERT: D 310 MET cc_start: 0.9156 (tpp) cc_final: 0.8951 (tpp) REVERT: D 982 MET cc_start: 0.8698 (mmm) cc_final: 0.7651 (mmm) REVERT: D 1056 LEU cc_start: 0.8931 (mt) cc_final: 0.8523 (mp) REVERT: D 1113 MET cc_start: 0.8702 (mmm) cc_final: 0.8471 (mmm) REVERT: D 1193 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8280 (mpt180) REVERT: F 180 ASN cc_start: 0.7773 (m110) cc_final: 0.7567 (m-40) REVERT: F 196 TYR cc_start: 0.8776 (t80) cc_final: 0.8573 (t80) REVERT: J 32 TYR cc_start: 0.8724 (m-80) cc_final: 0.8461 (m-80) REVERT: H 128 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7866 (tm-30) REVERT: H 135 LYS cc_start: 0.8985 (ptmm) cc_final: 0.8631 (tmtt) REVERT: H 505 GLN cc_start: 0.8671 (pp30) cc_final: 0.8338 (pp30) outliers start: 41 outliers final: 20 residues processed: 231 average time/residue: 0.4475 time to fit residues: 164.6990 Evaluate side-chains 200 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 274 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 342 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053799 restraints weight = 95042.206| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.11 r_work: 0.2790 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30001 Z= 0.200 Angle : 0.567 10.229 40858 Z= 0.298 Chirality : 0.042 0.230 4654 Planarity : 0.004 0.056 5226 Dihedral : 12.489 161.339 4624 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.68 % Allowed : 10.05 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3662 helix: 1.92 (0.14), residues: 1440 sheet: 0.24 (0.25), residues: 408 loop : -0.40 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 104 HIS 0.004 0.001 HIS D 853 PHE 0.015 0.001 PHE H 97 TYR 0.014 0.001 TYR C 722 ARG 0.006 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 1360) hydrogen bonds : angle 4.37106 ( 3830) metal coordination : bond 0.00952 ( 8) metal coordination : angle 3.88814 ( 12) covalent geometry : bond 0.00467 (29993) covalent geometry : angle 0.56280 (40846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9237 (tppt) cc_final: 0.8827 (tppt) REVERT: B 17 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 123 MET cc_start: 0.9022 (tmm) cc_final: 0.8783 (tmm) REVERT: C 203 LEU cc_start: 0.8370 (tp) cc_final: 0.8082 (mt) REVERT: C 461 LEU cc_start: 0.8730 (mp) cc_final: 0.8142 (tp) REVERT: C 772 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9051 (pp) REVERT: D 74 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8979 (tp) REVERT: D 982 MET cc_start: 0.8664 (mmm) cc_final: 0.7644 (mmm) REVERT: D 1113 MET cc_start: 0.8617 (mmm) cc_final: 0.8218 (mmm) REVERT: D 1193 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8327 (mpt180) REVERT: F 196 TYR cc_start: 0.8814 (t80) cc_final: 0.8599 (t80) REVERT: F 365 ILE cc_start: 0.8686 (tp) cc_final: 0.8421 (tt) REVERT: J 32 TYR cc_start: 0.8683 (m-80) cc_final: 0.8453 (m-80) REVERT: H 128 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7903 (tm-30) REVERT: H 135 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8626 (tmtt) REVERT: H 481 MET cc_start: 0.5498 (ptt) cc_final: 0.4853 (ptp) REVERT: H 505 GLN cc_start: 0.8721 (pp30) cc_final: 0.8309 (pp30) outliers start: 50 outliers final: 32 residues processed: 238 average time/residue: 0.4061 time to fit residues: 156.6150 Evaluate side-chains 212 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 214 GLN Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 211 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053558 restraints weight = 94342.404| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.08 r_work: 0.2799 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30001 Z= 0.194 Angle : 0.564 10.113 40858 Z= 0.296 Chirality : 0.042 0.283 4654 Planarity : 0.004 0.058 5226 Dihedral : 12.523 161.707 4624 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.05 % Allowed : 11.02 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3662 helix: 1.97 (0.14), residues: 1434 sheet: 0.14 (0.25), residues: 420 loop : -0.42 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 104 HIS 0.007 0.001 HIS F 454 PHE 0.018 0.001 PHE H 97 TYR 0.014 0.001 TYR C 722 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1360) hydrogen bonds : angle 4.29941 ( 3830) metal coordination : bond 0.00913 ( 8) metal coordination : angle 3.76689 ( 12) covalent geometry : bond 0.00455 (29993) covalent geometry : angle 0.55991 (40846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9275 (tppt) cc_final: 0.8909 (tppt) REVERT: B 17 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8678 (t0) REVERT: B 123 MET cc_start: 0.9045 (tmm) cc_final: 0.8797 (tmm) REVERT: C 203 LEU cc_start: 0.8380 (tp) cc_final: 0.8093 (mt) REVERT: C 461 LEU cc_start: 0.8726 (mp) cc_final: 0.8141 (tp) REVERT: C 772 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9063 (pp) REVERT: D 74 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8963 (tp) REVERT: D 143 MET cc_start: 0.7999 (ttp) cc_final: 0.7521 (tmm) REVERT: D 203 ARG cc_start: 0.7809 (mmm160) cc_final: 0.7192 (mmp80) REVERT: D 982 MET cc_start: 0.8663 (mmm) cc_final: 0.7668 (mmm) REVERT: D 1113 MET cc_start: 0.8594 (mmm) cc_final: 0.8174 (mmm) REVERT: F 196 TYR cc_start: 0.8853 (t80) cc_final: 0.8551 (t80) REVERT: F 339 LYS cc_start: 0.9335 (tppt) cc_final: 0.9132 (mmmt) REVERT: F 365 ILE cc_start: 0.8737 (tp) cc_final: 0.8475 (tt) REVERT: J 32 TYR cc_start: 0.8681 (m-80) cc_final: 0.8436 (m-80) REVERT: J 84 MET cc_start: 0.8802 (ttt) cc_final: 0.8474 (tpp) REVERT: H 135 LYS cc_start: 0.9024 (ptmm) cc_final: 0.8633 (tmtt) REVERT: H 481 MET cc_start: 0.5619 (ptt) cc_final: 0.5089 (ptp) REVERT: H 505 GLN cc_start: 0.8725 (pp30) cc_final: 0.8252 (pp30) outliers start: 61 outliers final: 43 residues processed: 251 average time/residue: 0.4268 time to fit residues: 170.8773 Evaluate side-chains 221 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1187 PHE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 192 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054307 restraints weight = 93254.848| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.22 r_work: 0.2811 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30001 Z= 0.120 Angle : 0.529 10.478 40858 Z= 0.276 Chirality : 0.041 0.235 4654 Planarity : 0.004 0.061 5226 Dihedral : 12.482 162.326 4624 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 11.83 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 3662 helix: 2.10 (0.14), residues: 1445 sheet: 0.13 (0.25), residues: 435 loop : -0.30 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 104 HIS 0.004 0.001 HIS F 454 PHE 0.015 0.001 PHE H 97 TYR 0.021 0.001 TYR H 113 ARG 0.005 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1360) hydrogen bonds : angle 4.08397 ( 3830) metal coordination : bond 0.00466 ( 8) metal coordination : angle 3.56297 ( 12) covalent geometry : bond 0.00275 (29993) covalent geometry : angle 0.52523 (40846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9291 (tppt) cc_final: 0.8947 (tppt) REVERT: B 16 GLU cc_start: 0.8230 (pm20) cc_final: 0.8019 (tp30) REVERT: B 17 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 123 MET cc_start: 0.9087 (tmm) cc_final: 0.8844 (tmm) REVERT: C 203 LEU cc_start: 0.8311 (tp) cc_final: 0.8030 (mt) REVERT: C 204 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: C 461 LEU cc_start: 0.8711 (mp) cc_final: 0.8122 (tp) REVERT: C 772 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8980 (pp) REVERT: D 83 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8628 (p) REVERT: D 155 MET cc_start: 0.7872 (tpt) cc_final: 0.7411 (tpt) REVERT: D 203 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7118 (mmp80) REVERT: D 982 MET cc_start: 0.8642 (mmm) cc_final: 0.7572 (mmm) REVERT: D 1113 MET cc_start: 0.8521 (mmm) cc_final: 0.8049 (mmm) REVERT: D 1193 ARG cc_start: 0.8035 (mmp80) cc_final: 0.6949 (mpt180) REVERT: F 196 TYR cc_start: 0.8762 (t80) cc_final: 0.8478 (t80) REVERT: F 365 ILE cc_start: 0.8763 (tp) cc_final: 0.8498 (tt) REVERT: J 32 TYR cc_start: 0.8692 (m-80) cc_final: 0.8409 (m-80) REVERT: H 41 GLU cc_start: 0.8348 (pt0) cc_final: 0.8051 (pp20) REVERT: H 135 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8689 (tmtt) REVERT: H 481 MET cc_start: 0.5574 (ptt) cc_final: 0.4994 (ptp) REVERT: H 505 GLN cc_start: 0.8714 (pp30) cc_final: 0.8231 (pp30) outliers start: 54 outliers final: 36 residues processed: 243 average time/residue: 0.4254 time to fit residues: 166.6732 Evaluate side-chains 216 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 149 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 166 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN C 832 HIS D 224 ASN D 287 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054226 restraints weight = 93447.344| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.21 r_work: 0.2811 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30001 Z= 0.127 Angle : 0.524 9.886 40858 Z= 0.273 Chirality : 0.041 0.247 4654 Planarity : 0.004 0.063 5226 Dihedral : 12.480 163.032 4624 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 12.03 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3662 helix: 2.16 (0.14), residues: 1444 sheet: 0.14 (0.26), residues: 428 loop : -0.29 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 104 HIS 0.003 0.001 HIS D 853 PHE 0.016 0.001 PHE H 97 TYR 0.011 0.001 TYR C 722 ARG 0.003 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1360) hydrogen bonds : angle 4.02258 ( 3830) metal coordination : bond 0.00526 ( 8) metal coordination : angle 3.33347 ( 12) covalent geometry : bond 0.00294 (29993) covalent geometry : angle 0.52047 (40846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9295 (tppt) cc_final: 0.8936 (tppt) REVERT: B 17 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 123 MET cc_start: 0.9121 (tmm) cc_final: 0.8893 (tmm) REVERT: C 145 MET cc_start: 0.8842 (mmm) cc_final: 0.8087 (mpp) REVERT: C 203 LEU cc_start: 0.8295 (tp) cc_final: 0.8005 (mt) REVERT: C 204 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: C 461 LEU cc_start: 0.8680 (mp) cc_final: 0.8098 (tp) REVERT: C 772 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8972 (pp) REVERT: D 83 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 155 MET cc_start: 0.7887 (tpt) cc_final: 0.7575 (tpt) REVERT: D 203 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7255 (mmp80) REVERT: D 982 MET cc_start: 0.8662 (mmm) cc_final: 0.7547 (mmm) REVERT: D 1113 MET cc_start: 0.8513 (mmm) cc_final: 0.8032 (mmm) REVERT: D 1162 MET cc_start: 0.9055 (mtt) cc_final: 0.8736 (mtt) REVERT: D 1193 ARG cc_start: 0.8064 (mmp80) cc_final: 0.6954 (mpt180) REVERT: F 339 LYS cc_start: 0.9362 (tppt) cc_final: 0.8999 (mttp) REVERT: F 365 ILE cc_start: 0.8759 (tp) cc_final: 0.8505 (tt) REVERT: J 32 TYR cc_start: 0.8675 (m-80) cc_final: 0.8436 (m-80) REVERT: J 94 LEU cc_start: 0.8580 (tp) cc_final: 0.8263 (mm) REVERT: H 41 GLU cc_start: 0.8321 (pt0) cc_final: 0.8037 (pp20) REVERT: H 135 LYS cc_start: 0.9073 (ptmm) cc_final: 0.8670 (tmtt) REVERT: H 505 GLN cc_start: 0.8729 (pp30) cc_final: 0.8245 (pp30) outliers start: 54 outliers final: 41 residues processed: 235 average time/residue: 0.4037 time to fit residues: 153.4249 Evaluate side-chains 220 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 292 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 367 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 361 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 364 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN C 133 ASN D 888 HIS ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN F 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.071707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.052070 restraints weight = 95041.409| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.21 r_work: 0.2754 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30001 Z= 0.246 Angle : 0.601 11.016 40858 Z= 0.313 Chirality : 0.043 0.233 4654 Planarity : 0.004 0.062 5226 Dihedral : 12.613 163.284 4624 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.02 % Allowed : 12.47 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3662 helix: 2.02 (0.14), residues: 1428 sheet: 0.06 (0.26), residues: 416 loop : -0.43 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 104 HIS 0.005 0.001 HIS D 853 PHE 0.021 0.002 PHE H 97 TYR 0.018 0.002 TYR F 196 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1360) hydrogen bonds : angle 4.26321 ( 3830) metal coordination : bond 0.01154 ( 8) metal coordination : angle 3.61007 ( 12) covalent geometry : bond 0.00577 (29993) covalent geometry : angle 0.59739 (40846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9310 (tppt) cc_final: 0.8941 (tppt) REVERT: B 5 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: B 17 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8010 (t0) REVERT: B 123 MET cc_start: 0.9097 (tmm) cc_final: 0.8851 (tmm) REVERT: C 772 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9102 (pp) REVERT: D 6 PHE cc_start: 0.8103 (t80) cc_final: 0.7691 (t80) REVERT: D 143 MET cc_start: 0.7899 (ttp) cc_final: 0.7399 (tmm) REVERT: D 155 MET cc_start: 0.7944 (tpt) cc_final: 0.7570 (tpt) REVERT: D 203 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7270 (mmp80) REVERT: D 215 GLU cc_start: 0.7041 (pt0) cc_final: 0.6802 (pt0) REVERT: D 982 MET cc_start: 0.8685 (mmm) cc_final: 0.7631 (mmm) REVERT: D 1113 MET cc_start: 0.8576 (mmm) cc_final: 0.8085 (mmm) REVERT: D 1162 MET cc_start: 0.9138 (mtt) cc_final: 0.8727 (mtt) REVERT: D 1193 ARG cc_start: 0.7992 (mmp80) cc_final: 0.6817 (mpt180) REVERT: F 365 ILE cc_start: 0.8802 (tp) cc_final: 0.8559 (tt) REVERT: J 32 TYR cc_start: 0.8730 (m-80) cc_final: 0.8511 (m-80) REVERT: H 135 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8705 (tmtt) REVERT: H 505 GLN cc_start: 0.8779 (pp30) cc_final: 0.8306 (pp30) outliers start: 60 outliers final: 48 residues processed: 229 average time/residue: 0.4068 time to fit residues: 151.8996 Evaluate side-chains 219 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 195 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 346 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054520 restraints weight = 93477.117| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.22 r_work: 0.2819 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30001 Z= 0.106 Angle : 0.523 10.905 40858 Z= 0.273 Chirality : 0.040 0.216 4654 Planarity : 0.004 0.063 5226 Dihedral : 12.516 164.285 4624 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.44 % Allowed : 13.04 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3662 helix: 2.19 (0.14), residues: 1446 sheet: 0.09 (0.26), residues: 433 loop : -0.32 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 104 HIS 0.003 0.001 HIS F 454 PHE 0.014 0.001 PHE H 97 TYR 0.012 0.001 TYR F 434 ARG 0.009 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 1360) hydrogen bonds : angle 3.95813 ( 3830) metal coordination : bond 0.00345 ( 8) metal coordination : angle 3.32501 ( 12) covalent geometry : bond 0.00237 (29993) covalent geometry : angle 0.52024 (40846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9315 (tppt) cc_final: 0.9041 (tppt) REVERT: B 17 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7919 (t0) REVERT: B 123 MET cc_start: 0.9139 (tmm) cc_final: 0.8912 (tmm) REVERT: C 772 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8969 (pp) REVERT: D 6 PHE cc_start: 0.8093 (t80) cc_final: 0.7672 (t80) REVERT: D 83 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8596 (p) REVERT: D 143 MET cc_start: 0.7799 (ttp) cc_final: 0.7308 (tmm) REVERT: D 155 MET cc_start: 0.8028 (tpt) cc_final: 0.7738 (tpt) REVERT: D 203 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7228 (mmp80) REVERT: D 982 MET cc_start: 0.8650 (mmm) cc_final: 0.7563 (mmm) REVERT: D 1113 MET cc_start: 0.8548 (mmm) cc_final: 0.8101 (mmm) REVERT: D 1162 MET cc_start: 0.9125 (mtt) cc_final: 0.8716 (mtt) REVERT: D 1193 ARG cc_start: 0.8057 (mmp80) cc_final: 0.6880 (mpt180) REVERT: F 287 TRP cc_start: 0.8609 (m100) cc_final: 0.8236 (m100) REVERT: F 365 ILE cc_start: 0.8794 (tp) cc_final: 0.8546 (tt) REVERT: J 7 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7244 (ttm-80) REVERT: H 41 GLU cc_start: 0.8339 (pt0) cc_final: 0.8039 (pp20) REVERT: H 128 GLN cc_start: 0.8780 (tp40) cc_final: 0.8263 (tp-100) REVERT: H 135 LYS cc_start: 0.9084 (ptmm) cc_final: 0.8726 (tmtt) REVERT: H 505 GLN cc_start: 0.8760 (pp30) cc_final: 0.8277 (pp30) outliers start: 43 outliers final: 32 residues processed: 227 average time/residue: 0.4086 time to fit residues: 149.5385 Evaluate side-chains 210 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 21 optimal weight: 5.9990 chunk 355 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS D 207 GLN D 287 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN F 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.050463 restraints weight = 95841.452| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.07 r_work: 0.2705 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 30001 Z= 0.406 Angle : 0.750 11.050 40858 Z= 0.392 Chirality : 0.048 0.246 4654 Planarity : 0.005 0.063 5226 Dihedral : 12.823 163.991 4624 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 1.61 % Allowed : 13.37 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3662 helix: 1.63 (0.13), residues: 1429 sheet: -0.18 (0.25), residues: 432 loop : -0.65 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 104 HIS 0.009 0.002 HIS D 103 PHE 0.028 0.002 PHE H 97 TYR 0.025 0.002 TYR E 75 ARG 0.012 0.001 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 1360) hydrogen bonds : angle 4.65597 ( 3830) metal coordination : bond 0.01856 ( 8) metal coordination : angle 4.09138 ( 12) covalent geometry : bond 0.00944 (29993) covalent geometry : angle 0.74731 (40846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7324 Ramachandran restraints generated. 3662 Oldfield, 0 Emsley, 3662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.7806 (t0) REVERT: B 123 MET cc_start: 0.9036 (tmm) cc_final: 0.8801 (tmm) REVERT: C 772 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9188 (pp) REVERT: D 6 PHE cc_start: 0.8076 (t80) cc_final: 0.7709 (t80) REVERT: D 143 MET cc_start: 0.7965 (ttp) cc_final: 0.7485 (tmm) REVERT: D 155 MET cc_start: 0.7959 (tpt) cc_final: 0.7664 (tpt) REVERT: D 203 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7379 (mmp80) REVERT: D 215 GLU cc_start: 0.7081 (pt0) cc_final: 0.6833 (pt0) REVERT: D 1113 MET cc_start: 0.8587 (mmm) cc_final: 0.8120 (mmm) REVERT: D 1162 MET cc_start: 0.9198 (mtt) cc_final: 0.8923 (mtt) REVERT: E 75 TYR cc_start: 0.7654 (m-80) cc_final: 0.7437 (m-80) REVERT: F 196 TYR cc_start: 0.9076 (t80) cc_final: 0.8873 (t80) REVERT: F 219 MET cc_start: 0.7949 (tmm) cc_final: 0.7686 (tmm) REVERT: J 7 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7304 (ttm-80) REVERT: J 32 TYR cc_start: 0.8779 (m-80) cc_final: 0.8409 (m-80) REVERT: H 110 ARG cc_start: 0.8580 (tpm170) cc_final: 0.8216 (mmm160) REVERT: H 135 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8706 (tmtt) REVERT: H 505 GLN cc_start: 0.8849 (pp30) cc_final: 0.8390 (pp30) outliers start: 48 outliers final: 43 residues processed: 214 average time/residue: 0.4310 time to fit residues: 148.5813 Evaluate side-chains 207 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1054 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain H residue 130 HIS Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 14 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.053848 restraints weight = 93274.495| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.28 r_work: 0.2785 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30001 Z= 0.125 Angle : 0.558 10.886 40858 Z= 0.292 Chirality : 0.041 0.221 4654 Planarity : 0.004 0.064 5226 Dihedral : 12.662 164.654 4624 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.48 % Allowed : 13.44 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3662 helix: 2.00 (0.14), residues: 1440 sheet: -0.11 (0.25), residues: 431 loop : -0.46 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 104 HIS 0.003 0.001 HIS D 505 PHE 0.016 0.001 PHE H 97 TYR 0.021 0.001 TYR E 75 ARG 0.011 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1360) hydrogen bonds : angle 4.14585 ( 3830) metal coordination : bond 0.00485 ( 8) metal coordination : angle 3.72611 ( 12) covalent geometry : bond 0.00282 (29993) covalent geometry : angle 0.55432 (40846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11319.55 seconds wall clock time: 197 minutes 29.55 seconds (11849.55 seconds total)