Starting phenix.real_space_refine on Mon Dec 30 02:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3i_18128/12_2024/8q3i_18128.cif" } resolution = 3.11 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 Mg 1 5.21 5 S 106 5.16 5 C 18868 2.51 5 N 5372 2.21 5 O 5791 1.98 5 H 30177 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 1.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 60317 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3475 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3574 Classifications: {'peptide': 233} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Chain: "C" Number of atoms: 16846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 16846 Classifications: {'peptide': 1093} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1034} Chain breaks: 1 Chain: "D" Number of atoms: 20036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 20036 Classifications: {'peptide': 1272} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1214} Chain breaks: 1 Chain: "E" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1167 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Chain: "F" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3560 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 10601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 10601 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 37, 'TRANS': 652} Chain breaks: 1 Chain: "J" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1055 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38102 SG CYS D 890 37.044 57.940 76.338 1.00 30.12 S ATOM 39227 SG CYS D 967 40.134 59.865 77.596 1.00 21.56 S ATOM 39309 SG CYS D 974 37.367 58.745 79.971 1.00 21.41 S ATOM 39346 SG CYS D 977 39.589 56.328 78.599 1.00 24.18 S ATOM 24832 SG CYS D 60 32.098 120.933 89.523 1.00 66.14 S ATOM 24863 SG CYS D 62 32.071 124.506 88.601 1.00 69.42 S ATOM 25096 SG CYS D 75 29.991 122.123 86.938 1.00 68.34 S ATOM 25145 SG CYS D 78 33.534 121.788 86.341 1.00 62.33 S Time building chain proxies: 21.33, per 1000 atoms: 0.35 Number of scatterers: 60317 At special positions: 0 Unit cell: (144.725, 162.919, 173.67, 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 106 16.00 Mg 1 11.99 O 5791 8.00 N 5372 7.00 C 18868 6.00 H 30177 1.00 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: 12.28 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 46 sheets defined 45.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 4.112A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.529A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.566A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 225' Processing helix chain 'B' and resid 30 through 45 removed outlier: 4.298A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.375A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 removed outlier: 4.179A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.546A pdb=" N GLU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 371 through 395 removed outlier: 3.616A pdb=" N GLN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.531A pdb=" N ILE C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.668A pdb=" N ARG C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.577A pdb=" N TYR C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 540 through 544 removed outlier: 4.089A pdb=" N ARG C 544 " --> pdb=" O GLU C 541 " (cutoff:3.500A) 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 579 through 584 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.741A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 605 " --> pdb=" O ASN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.633A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.662A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 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 909 through 911 No H-bonds generated for 'chain 'C' and resid 909 through 911' Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1050 through 1054 removed outlier: 4.209A pdb=" N PHE C1054 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1087 through 1100 Processing helix chain 'C' and resid 1109 through 1122 removed outlier: 3.713A pdb=" N LEU C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 187 removed outlier: 5.234A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.610A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.638A pdb=" N SER D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.677A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 304 removed outlier: 4.173A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.602A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 338 through 361 removed outlier: 4.329A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.822A pdb=" N GLY D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 4.669A pdb=" N ASN D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.676A pdb=" N ARG D 459 " --> pdb=" O PHE D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 478 removed outlier: 3.975A pdb=" N ARG D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.868A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.782A 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 651 removed outlier: 3.677A pdb=" N ALA D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.518A pdb=" N ASP D 713 " --> pdb=" O ALA D 709 " (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: 3.623A 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: 4.079A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 862 " --> pdb=" O GLY D 858 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 4.301A pdb=" N GLU D 916 " --> pdb=" O ALA D 913 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N VAL D 997 " --> pdb=" O ALA D 993 " (cutoff:3.500A) 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 1146 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.993A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D1162 " --> pdb=" O ILE D1158 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1163 " --> pdb=" O VAL D1159 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1197 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1248 through 1256 removed outlier: 3.813A pdb=" N ASN D1252 " --> pdb=" O GLY D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1282 Processing helix 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 removed outlier: 3.528A pdb=" N ILE E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'F' and resid 143 through 157 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 212 through 236 removed outlier: 3.590A pdb=" N ASP F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG F 224 " --> pdb=" O GLN F 220 " (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 298 removed outlier: 3.807A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 310 through 329 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 344 through 354 removed outlier: 3.683A pdb=" N GLN F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 42 removed outlier: 3.641A pdb=" N HIS H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 66 Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.820A 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 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 175 through 188 Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 220 through 225 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 258 through 262 removed outlier: 3.888A pdb=" N PHE H 262 " --> pdb=" O PRO H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 282 Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.886A pdb=" N VAL H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 removed outlier: 3.887A pdb=" N GLY H 331 " --> pdb=" O ALA H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 358 removed outlier: 4.938A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 383 removed outlier: 3.729A pdb=" N ASP H 383 " --> pdb=" O GLY H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 395 Processing helix chain 'H' and resid 399 through 410 removed outlier: 3.607A pdb=" N SER H 410 " --> pdb=" O GLN H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 418 Processing helix chain 'H' and resid 420 through 424 Processing helix chain 'H' and resid 434 through 447 removed outlier: 4.394A pdb=" N LEU H 438 " --> pdb=" O SER H 434 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 469 Processing helix chain 'H' and resid 470 through 474 Processing helix chain 'H' and resid 509 through 517 removed outlier: 3.852A pdb=" N ASP H 517 " --> pdb=" O ARG H 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 533 Processing helix chain 'H' and resid 534 through 544 Processing helix chain 'H' and resid 555 through 559 Processing helix chain 'H' and resid 567 through 573 removed outlier: 3.734A pdb=" N MET H 571 " --> pdb=" O SER H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 607 removed outlier: 3.892A pdb=" N VAL H 598 " --> pdb=" O GLU H 594 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 647 removed outlier: 4.403A pdb=" N SER H 635 " --> pdb=" O ASP H 631 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY H 646 " --> pdb=" O SER H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 664 through 669 Processing helix chain 'H' and resid 680 through 685 Processing helix chain 'H' and resid 690 through 701 removed outlier: 3.526A pdb=" N GLU H 694 " --> pdb=" O ARG H 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 removed outlier: 3.669A pdb=" N GLU J 87 " --> pdb=" O ASP J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.757A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.384A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.280A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.536A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.403A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.486A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.698A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB4, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.326A pdb=" N SER C 168 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 182 removed outlier: 3.763A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.444A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.625A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.411A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.760A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC3, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.414A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.286A 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=AC4, first strand: chain 'C' and resid 756 through 757 removed outlier: 6.449A pdb=" N SER C 740 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 867 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS C 742 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA C 865 " --> pdb=" O HIS C 742 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 744 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR C 863 " --> pdb=" O GLU C 744 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N HIS C 746 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG C 861 " --> pdb=" O HIS C 746 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 748 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 859 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 750 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 759 through 760 removed outlier: 3.559A pdb=" N THR C 798 " --> pdb=" O ARG C 824 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.636A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC8, first strand: chain 'C' and resid 1033 through 1034 removed outlier: 6.381A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.663A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1133 through 1134 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.592A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.935A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD5, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD6, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD7, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AD8, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.744A pdb=" N ILE D 910 " --> pdb=" O GLU D 902 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 928 through 929 removed outlier: 6.685A pdb=" N ALA D 928 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE2, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 5.752A pdb=" N VAL D1077 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D1067 " --> pdb=" O VAL D1077 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP D1079 " --> pdb=" O ILE D1065 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D1065 " --> pdb=" O ASP D1079 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 6.731A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE5, first strand: chain 'H' and resid 90 through 91 removed outlier: 9.499A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU H 83 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG H 74 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE H 85 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE H 72 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN H 128 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG H 74 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG H 126 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP H 76 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU H 132 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 254 through 257 removed outlier: 3.600A pdb=" N ASP H 528 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL H 525 " --> pdb=" O THR H 551 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL H 553 " --> pdb=" O VAL H 525 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL H 527 " --> pdb=" O VAL H 553 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL H 194 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS H 583 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL H 196 " --> pdb=" O LYS H 583 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AE8, first strand: chain 'H' and resid 587 through 588 Processing sheet with id=AE9, first strand: chain 'H' and resid 624 through 626 removed outlier: 7.976A pdb=" N ASP H 674 " --> pdb=" O GLN H 704 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 706 " --> pdb=" O ASP H 674 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL H 676 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL H 708 " --> pdb=" O VAL H 676 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL H 678 " --> pdb=" O VAL H 708 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 39 through 45 1413 hydrogen bonds defined for protein. 3987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 25.61 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30161 1.03 - 1.23: 29 1.23 - 1.42: 12394 1.42 - 1.62: 18056 1.62 - 1.81: 188 Bond restraints: 60828 Sorted by residual: bond pdb=" CB PRO A 7 " pdb=" CG PRO A 7 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.07e+00 bond pdb=" CB ARG C1090 " pdb=" CG ARG C1090 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" N PRO A 7 " pdb=" CA PRO A 7 " ideal model delta sigma weight residual 1.469 1.453 0.016 1.28e-02 6.10e+03 1.47e+00 bond pdb=" C GLN C1046 " pdb=" N PRO C1047 " ideal model delta sigma weight residual 1.331 1.346 -0.014 1.21e-02 6.83e+03 1.39e+00 bond pdb=" CA ASN B 152 " pdb=" CB ASN B 152 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.62e-02 3.81e+03 1.30e+00 ... (remaining 60823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 108112 1.51 - 3.02: 1934 3.02 - 4.54: 191 4.54 - 6.05: 10 6.05 - 7.56: 5 Bond angle restraints: 110252 Sorted by residual: angle pdb=" CA PRO A 7 " pdb=" N PRO A 7 " pdb=" CD PRO A 7 " ideal model delta sigma weight residual 112.00 104.85 7.15 1.40e+00 5.10e-01 2.61e+01 angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 113.53 109.36 4.17 9.80e-01 1.04e+00 1.81e+01 angle pdb=" C LYS A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta sigma weight residual 124.82 132.38 -7.56 1.78e+00 3.16e-01 1.80e+01 angle pdb=" N VAL B 183 " pdb=" CA VAL B 183 " pdb=" C VAL B 183 " ideal model delta sigma weight residual 113.53 109.50 4.03 9.80e-01 1.04e+00 1.69e+01 angle pdb=" C GLN B 151 " pdb=" N ASN B 152 " pdb=" CA ASN B 152 " ideal model delta sigma weight residual 122.07 126.92 -4.85 1.43e+00 4.89e-01 1.15e+01 ... (remaining 110247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 25869 17.96 - 35.91: 1716 35.91 - 53.87: 542 53.87 - 71.83: 152 71.83 - 89.79: 38 Dihedral angle restraints: 28317 sinusoidal: 15922 harmonic: 12395 Sorted by residual: dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR C1044 " pdb=" C THR C1044 " pdb=" N GLN C1045 " pdb=" CA GLN C1045 " ideal model delta harmonic sigma weight residual -180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA TYR D1078 " pdb=" C TYR D1078 " pdb=" N ASP D1079 " pdb=" CA ASP D1079 " ideal model delta harmonic sigma weight residual -180.00 -159.55 -20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 28314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3073 0.031 - 0.062: 1055 0.062 - 0.092: 314 0.092 - 0.123: 220 0.123 - 0.154: 47 Chirality restraints: 4709 Sorted by residual: chirality pdb=" CA VAL D1068 " pdb=" N VAL D1068 " pdb=" C VAL D1068 " pdb=" CB VAL D1068 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-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 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 4706 not shown) Planarity restraints: 9156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 6 " -0.093 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO A 7 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 7 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 7 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1090 " 0.477 9.50e-02 1.11e+02 1.59e-01 2.91e+01 pdb=" NE ARG C1090 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C1090 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C1090 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C1090 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG C1090 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C1090 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C1090 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C1090 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 151 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C GLN B 151 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN B 151 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 152 " 0.013 2.00e-02 2.50e+03 ... (remaining 9153 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1853 2.14 - 2.76: 114899 2.76 - 3.37: 172573 3.37 - 3.99: 220467 3.99 - 4.60: 347934 Nonbonded interactions: 857726 Sorted by model distance: nonbonded pdb=" H LEU D 330 " pdb=" O ARG D 334 " model vdw 1.529 2.450 nonbonded pdb=" H GLY B 29 " pdb=" OD2 ASP B 190 " model vdw 1.547 2.450 nonbonded pdb=" HE ARG B 20 " pdb=" OD1 ASP B 195 " model vdw 1.575 2.450 nonbonded pdb="HH21 ARG D 113 " pdb=" OD1 ASP D1236 " model vdw 1.586 2.450 nonbonded pdb="HH12 ARG A 40 " pdb=" OD1 ASP C 894 " model vdw 1.607 2.450 ... (remaining 857721 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.820 Extract box with map and model: 1.860 Check model and map are aligned: 0.350 Set scattering table: 0.420 Process input model: 121.540 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.002 0.101 30651 Z= 0.148 Angle : 0.553 7.559 41530 Z= 0.314 Chirality : 0.041 0.154 4709 Planarity : 0.005 0.216 5491 Dihedral : 14.018 89.786 11623 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.84 (0.13), residues: 3846 helix: 1.21 (0.13), residues: 1513 sheet: 0.46 (0.23), residues: 445 loop : 0.17 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 322 HIS 0.006 0.001 HIS D 748 PHE 0.030 0.001 PHE C 364 TYR 0.030 0.001 TYR C1040 ARG 0.011 0.000 ARG C1090 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 1.0410 time to fit residues: 526.4573 Evaluate side-chains 200 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN E 66 ASN J 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30651 Z= 0.236 Angle : 0.538 5.626 41530 Z= 0.292 Chirality : 0.042 0.147 4709 Planarity : 0.005 0.084 5491 Dihedral : 4.561 24.059 4254 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.37 % Allowed : 3.41 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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 (0.13), residues: 3846 helix: 1.36 (0.13), residues: 1535 sheet: 0.41 (0.24), residues: 440 loop : 0.09 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 929 HIS 0.004 0.001 HIS D 748 PHE 0.021 0.001 PHE D 920 TYR 0.017 0.001 TYR C 722 ARG 0.007 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 212 average time/residue: 0.8834 time to fit residues: 292.6682 Evaluate side-chains 201 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Chi-restraints excluded: chain J residue 28 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 4.9990 chunk 108 optimal weight: 0.0870 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30651 Z= 0.205 Angle : 0.496 5.401 41530 Z= 0.266 Chirality : 0.041 0.138 4709 Planarity : 0.004 0.067 5491 Dihedral : 4.361 23.577 4254 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.40 % Allowed : 3.91 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.97 (0.14), residues: 3846 helix: 1.53 (0.13), residues: 1540 sheet: 0.28 (0.23), residues: 453 loop : 0.08 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 929 HIS 0.004 0.001 HIS D 748 PHE 0.017 0.001 PHE H 606 TYR 0.011 0.001 TYR C 722 ARG 0.004 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 687 MET cc_start: 0.8000 (mmp) cc_final: 0.7740 (mmp) outliers start: 13 outliers final: 10 residues processed: 205 average time/residue: 0.9268 time to fit residues: 298.1235 Evaluate side-chains 200 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 730 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30651 Z= 0.301 Angle : 0.519 8.522 41530 Z= 0.278 Chirality : 0.042 0.211 4709 Planarity : 0.004 0.067 5491 Dihedral : 4.326 24.661 4254 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.43 % Allowed : 5.06 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.93 (0.13), residues: 3846 helix: 1.53 (0.13), residues: 1547 sheet: 0.17 (0.23), residues: 439 loop : 0.04 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 929 HIS 0.005 0.001 HIS D 748 PHE 0.019 0.002 PHE C 364 TYR 0.013 0.001 TYR C 722 ARG 0.012 0.000 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 207 average time/residue: 0.8518 time to fit residues: 278.3210 Evaluate side-chains 196 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Chi-restraints excluded: chain J residue 28 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30651 Z= 0.267 Angle : 0.498 5.643 41530 Z= 0.268 Chirality : 0.042 0.145 4709 Planarity : 0.004 0.064 5491 Dihedral : 4.249 24.315 4254 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.31 % Allowed : 6.49 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.01 (0.14), residues: 3846 helix: 1.64 (0.13), residues: 1549 sheet: 0.11 (0.23), residues: 449 loop : 0.07 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1221 HIS 0.005 0.001 HIS D 748 PHE 0.017 0.001 PHE H 606 TYR 0.011 0.001 TYR C 335 ARG 0.005 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 3.785 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: 10 outliers final: 10 residues processed: 195 average time/residue: 0.8749 time to fit residues: 267.2860 Evaluate side-chains 192 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.0670 chunk 308 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 30651 Z= 0.261 Angle : 0.492 4.728 41530 Z= 0.263 Chirality : 0.041 0.145 4709 Planarity : 0.004 0.062 5491 Dihedral : 4.189 23.920 4254 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.34 % Allowed : 6.86 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.06 (0.14), residues: 3846 helix: 1.72 (0.13), residues: 1552 sheet: 0.13 (0.23), residues: 445 loop : 0.06 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 722 HIS 0.005 0.001 HIS D 748 PHE 0.017 0.001 PHE H 606 TYR 0.011 0.001 TYR C 722 ARG 0.005 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLN cc_start: 0.7663 (pm20) cc_final: 0.7220 (pm20) outliers start: 11 outliers final: 9 residues processed: 196 average time/residue: 0.8786 time to fit residues: 271.6129 Evaluate side-chains 191 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30651 Z= 0.203 Angle : 0.474 7.075 41530 Z= 0.252 Chirality : 0.041 0.138 4709 Planarity : 0.004 0.061 5491 Dihedral : 4.086 23.405 4254 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.34 % Allowed : 7.20 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.17 (0.14), residues: 3846 helix: 1.84 (0.13), residues: 1556 sheet: 0.13 (0.23), residues: 447 loop : 0.10 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 722 HIS 0.005 0.001 HIS D 748 PHE 0.017 0.001 PHE H 606 TYR 0.010 0.001 TYR C 335 ARG 0.005 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 3.941 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: 11 outliers final: 9 residues processed: 191 average time/residue: 0.8589 time to fit residues: 258.6500 Evaluate side-chains 189 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 221 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30651 Z= 0.178 Angle : 0.463 5.732 41530 Z= 0.245 Chirality : 0.040 0.140 4709 Planarity : 0.004 0.057 5491 Dihedral : 3.978 22.478 4254 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.22 % Allowed : 7.67 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.30 (0.14), residues: 3846 helix: 1.98 (0.13), residues: 1557 sheet: 0.18 (0.23), residues: 447 loop : 0.16 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 722 HIS 0.005 0.001 HIS D 748 PHE 0.018 0.001 PHE H 606 TYR 0.012 0.001 TYR C 648 ARG 0.005 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLN cc_start: 0.7643 (pm20) cc_final: 0.7245 (pm20) REVERT: D 687 MET cc_start: 0.8085 (mmp) cc_final: 0.7665 (mmp) outliers start: 7 outliers final: 7 residues processed: 193 average time/residue: 0.9541 time to fit residues: 289.4742 Evaluate side-chains 190 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.3980 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 30651 Z= 0.250 Angle : 0.478 5.720 41530 Z= 0.254 Chirality : 0.041 0.142 4709 Planarity : 0.004 0.059 5491 Dihedral : 3.990 22.352 4254 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.28 % Allowed : 7.85 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.29 (0.14), residues: 3846 helix: 1.98 (0.13), residues: 1551 sheet: 0.14 (0.23), residues: 449 loop : 0.14 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1221 HIS 0.005 0.001 HIS D 748 PHE 0.018 0.001 PHE H 606 TYR 0.010 0.001 TYR C 335 ARG 0.004 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLN cc_start: 0.7697 (pm20) cc_final: 0.7253 (pm20) REVERT: D 687 MET cc_start: 0.8082 (mmp) cc_final: 0.7676 (mmp) outliers start: 9 outliers final: 9 residues processed: 188 average time/residue: 0.8508 time to fit residues: 251.0857 Evaluate side-chains 187 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 178 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 352 optimal weight: 0.5980 chunk 304 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 186 optimal weight: 0.1980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30651 Z= 0.211 Angle : 0.475 12.169 41530 Z= 0.250 Chirality : 0.041 0.138 4709 Planarity : 0.004 0.058 5491 Dihedral : 3.969 21.719 4254 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.28 % Allowed : 7.88 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.33 (0.14), residues: 3846 helix: 2.00 (0.13), residues: 1563 sheet: 0.21 (0.23), residues: 444 loop : 0.16 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1221 HIS 0.004 0.001 HIS D 748 PHE 0.018 0.001 PHE H 606 TYR 0.011 0.001 TYR C 335 ARG 0.006 0.000 ARG D 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 33 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 3.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 687 MET cc_start: 0.8066 (mmp) cc_final: 0.7689 (mmp) outliers start: 9 outliers final: 9 residues processed: 184 average time/residue: 0.8785 time to fit residues: 253.0529 Evaluate side-chains 189 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 1015 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 606 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 313 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060613 restraints weight = 270030.513| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.91 r_work: 0.2855 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30651 Z= 0.168 Angle : 0.461 8.465 41530 Z= 0.243 Chirality : 0.040 0.141 4709 Planarity : 0.004 0.074 5491 Dihedral : 3.891 20.473 4254 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.28 % Allowed : 7.88 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 1.43 (0.14), residues: 3846 helix: 2.10 (0.13), residues: 1564 sheet: 0.26 (0.23), residues: 444 loop : 0.21 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 722 HIS 0.004 0.001 HIS D 748 PHE 0.018 0.001 PHE H 606 TYR 0.010 0.001 TYR C 335 ARG 0.009 0.000 ARG D 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9191.59 seconds wall clock time: 159 minutes 46.10 seconds (9586.10 seconds total)