Starting phenix.real_space_refine on Thu Nov 20 05:13:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yke_6831/11_2025/5yke_6831.map" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 188 5.16 5 Cl 4 4.86 5 C 20196 2.51 5 N 5116 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30636 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 7.85, per 1000 atoms: 0.26 Number of scatterers: 30636 At special positions: 0 Unit cell: (174.075, 174.075, 110.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 188 16.00 O 5132 8.00 N 5116 7.00 C 20196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7472 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 87.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'B' and resid 25 through 52 Proline residue: B 35 - end of helix removed outlier: 3.942A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 70 through 96 Processing helix chain 'B' and resid 104 through 130 Proline residue: B 109 - end of helix removed outlier: 3.757A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 193 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.595A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.447A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix removed outlier: 3.575A pdb=" N THR B1161 " --> pdb=" O ILE B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU B1165 " --> pdb=" O THR B1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL B1281 " --> pdb=" O SER B1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'D' and resid 25 through 52 Proline residue: D 35 - end of helix removed outlier: 3.942A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 70 through 96 Processing helix chain 'D' and resid 104 through 130 Proline residue: D 109 - end of helix removed outlier: 3.757A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 193 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 423 through 457 Proline residue: D 436 - end of helix removed outlier: 3.536A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.595A pdb=" N GLU D 501 " --> pdb=" O LYS D 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.447A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS D1001 " --> pdb=" O PRO D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU D1013 " --> pdb=" O GLY D1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1116 Processing helix chain 'D' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE D1121 " --> pdb=" O PRO D1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1161 Proline residue: D1137 - end of helix removed outlier: 3.575A pdb=" N THR D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU D1165 " --> pdb=" O THR D1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.525A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1218 Processing helix chain 'D' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL D1281 " --> pdb=" O SER D1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'F' and resid 25 through 52 Proline residue: F 35 - end of helix removed outlier: 3.942A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 70 through 96 Processing helix chain 'F' and resid 104 through 130 Proline residue: F 109 - end of helix removed outlier: 3.757A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 423 through 457 Proline residue: F 436 - end of helix removed outlier: 3.536A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.595A pdb=" N GLU F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.447A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS F1001 " --> pdb=" O PRO F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP F1039 " --> pdb=" O ALA F1035 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU F1107 " --> pdb=" O ASN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1116 Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE F1121 " --> pdb=" O PRO F1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1161 Proline residue: F1137 - end of helix removed outlier: 3.575A pdb=" N THR F1161 " --> pdb=" O ILE F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU F1165 " --> pdb=" O THR F1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.525A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL F1281 " --> pdb=" O SER F1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'H' and resid 25 through 52 Proline residue: H 35 - end of helix removed outlier: 3.942A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 70 through 96 Processing helix chain 'H' and resid 104 through 130 Proline residue: H 109 - end of helix removed outlier: 3.757A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE H 137 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 193 Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 402 " --> pdb=" O LYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 423 through 457 Proline residue: H 436 - end of helix removed outlier: 3.536A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.595A pdb=" N GLU H 501 " --> pdb=" O LYS H 497 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA H 576 " --> pdb=" O SER H 572 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.447A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.533A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP H1039 " --> pdb=" O ALA H1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1107 removed outlier: 3.541A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 Processing helix chain 'H' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1161 Proline residue: H1137 - end of helix removed outlier: 3.575A pdb=" N THR H1161 " --> pdb=" O ILE H1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU H1165 " --> pdb=" O THR H1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.525A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL H1281 " --> pdb=" O SER H1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) 2472 hydrogen bonds defined for protein. 7392 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: 5.61 Time building geometry restraints manager: 3.96 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: 8600 1.34 - 1.46: 6252 1.46 - 1.58: 16160 1.58 - 1.70: 8 1.70 - 1.82: 292 Bond restraints: 31312 Sorted by residual: bond pdb=" C18 GBM B2001 " pdb=" S2 GBM B2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM D2001 " pdb=" S2 GBM D2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM F2001 " pdb=" S2 GBM F2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM H2001 " pdb=" S2 GBM H2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C27 GBM F2001 " pdb=" C28 GBM F2001 " ideal model delta sigma weight residual 1.401 1.490 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 31307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 41684 2.40 - 4.80: 728 4.80 - 7.20: 140 7.20 - 9.60: 20 9.60 - 12.00: 16 Bond angle restraints: 42588 Sorted by residual: angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR D 200 " pdb=" CA THR D 200 " pdb=" C THR D 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR H 200 " pdb=" CA THR H 200 " pdb=" C THR H 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR F 200 " pdb=" CA THR F 200 " pdb=" C THR F 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" C SER D 532 " pdb=" N LEU D 533 " pdb=" CA LEU D 533 " ideal model delta sigma weight residual 120.28 130.85 -10.57 1.44e+00 4.82e-01 5.38e+01 ... (remaining 42583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 16888 16.66 - 33.32: 1056 33.32 - 49.99: 344 49.99 - 66.65: 104 66.65 - 83.31: 24 Dihedral angle restraints: 18416 sinusoidal: 6960 harmonic: 11456 Sorted by residual: dihedral pdb=" CA PHE D 295 " pdb=" C PHE D 295 " pdb=" N GLY D 296 " pdb=" CA GLY D 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE F 295 " pdb=" C PHE F 295 " pdb=" N GLY F 296 " pdb=" CA GLY F 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 18413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4420 0.058 - 0.117: 692 0.117 - 0.175: 44 0.175 - 0.233: 16 0.233 - 0.292: 24 Chirality restraints: 5196 Sorted by residual: chirality pdb=" CA ASP B1133 " pdb=" N ASP B1133 " pdb=" C ASP B1133 " pdb=" CB ASP B1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP F1133 " pdb=" N ASP F1133 " pdb=" C ASP F1133 " pdb=" CB ASP F1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP D1133 " pdb=" N ASP D1133 " pdb=" C ASP D1133 " pdb=" CB ASP D1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5193 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM H2001 " -0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM H2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM H2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM H2001 " 0.478 2.00e-02 2.50e+03 pdb=" O6 GBM H2001 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM D2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM D2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM D2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM D2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM D2001 " 0.063 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6484 2.78 - 3.31: 32596 3.31 - 3.84: 51016 3.84 - 4.37: 55778 4.37 - 4.90: 94232 Nonbonded interactions: 240106 Sorted by model distance: nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP H1031 " pdb=" OH TYR H1287 " model vdw 2.246 3.040 nonbonded pdb=" O SER F1126 " pdb=" ND2 ASN F1130 " model vdw 2.276 3.120 ... (remaining 240101 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.005 0.162 31316 Z= 0.269 Angle : 0.809 12.002 42596 Z= 0.463 Chirality : 0.046 0.292 5196 Planarity : 0.010 0.272 5116 Dihedral : 13.613 83.309 10932 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.65 % Favored : 95.93 % Rotamer: Outliers : 7.60 % Allowed : 10.29 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.12), residues: 3832 helix: -0.74 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 598 TYR 0.014 0.002 TYR D 378 PHE 0.034 0.002 PHE A 168 TRP 0.010 0.001 TRP B1037 HIS 0.011 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00514 (31312) covalent geometry : angle 0.80886 (42588) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.10088 ( 8) hydrogen bonds : bond 0.14835 ( 2472) hydrogen bonds : angle 6.13023 ( 7392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 930 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7945 (tptt) cc_final: 0.6948 (mptt) REVERT: A 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: A 152 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8634 (tp40) REVERT: A 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7261 (mtt180) REVERT: A 177 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: B 51 TRP cc_start: 0.7652 (t60) cc_final: 0.6544 (m-10) REVERT: B 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8666 (m-10) REVERT: B 136 LEU cc_start: 0.8057 (mt) cc_final: 0.7533 (pp) REVERT: B 157 PHE cc_start: 0.7468 (t80) cc_final: 0.6641 (t80) REVERT: B 158 TYR cc_start: 0.8838 (t80) cc_final: 0.8618 (t80) REVERT: B 181 MET cc_start: 0.9001 (mtp) cc_final: 0.8524 (mmt) REVERT: B 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8689 (tt) REVERT: B 186 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7760 (tp30) REVERT: B 233 MET cc_start: 0.9260 (mmm) cc_final: 0.9004 (mmm) REVERT: B 382 GLU cc_start: 0.8066 (tt0) cc_final: 0.7681 (tt0) REVERT: B 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6979 (t70) REVERT: B 1031 ASP cc_start: 0.8795 (m-30) cc_final: 0.8487 (p0) REVERT: B 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7443 (m-80) REVERT: B 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 1171 LEU cc_start: 0.8464 (mt) cc_final: 0.8260 (pp) REVERT: B 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8780 (mmp80) REVERT: B 1252 MET cc_start: 0.9034 (ttm) cc_final: 0.8720 (mmt) REVERT: C 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: C 131 ILE cc_start: 0.8712 (pt) cc_final: 0.8497 (mt) REVERT: C 152 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8629 (tp40) REVERT: C 176 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7261 (mtt180) REVERT: C 177 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.6759 (ttp-170) REVERT: D 51 TRP cc_start: 0.7654 (t60) cc_final: 0.6548 (m-10) REVERT: D 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8664 (m-10) REVERT: D 136 LEU cc_start: 0.8059 (mt) cc_final: 0.7530 (pp) REVERT: D 157 PHE cc_start: 0.7467 (t80) cc_final: 0.6640 (t80) REVERT: D 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8617 (t80) REVERT: D 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8524 (mmt) REVERT: D 184 LEU cc_start: 0.9346 (mt) cc_final: 0.8691 (tt) REVERT: D 186 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 233 MET cc_start: 0.9261 (mmm) cc_final: 0.9007 (mmm) REVERT: D 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7671 (tt0) REVERT: D 570 ASP cc_start: 0.7539 (m-30) cc_final: 0.6982 (t70) REVERT: D 1031 ASP cc_start: 0.8797 (m-30) cc_final: 0.8485 (p0) REVERT: D 1064 TYR cc_start: 0.7668 (m-80) cc_final: 0.7442 (m-80) REVERT: D 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8032 (tp) REVERT: D 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8261 (pp) REVERT: D 1246 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8782 (mmp80) REVERT: D 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8721 (mmt) REVERT: E 91 TRP cc_start: 0.9119 (t60) cc_final: 0.8852 (t-100) REVERT: E 152 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8630 (tp40) REVERT: E 176 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7256 (mtt180) REVERT: E 177 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: F 51 TRP cc_start: 0.7650 (t60) cc_final: 0.6544 (m-10) REVERT: F 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8663 (m-10) REVERT: F 136 LEU cc_start: 0.8064 (mt) cc_final: 0.7536 (pp) REVERT: F 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6645 (t80) REVERT: F 158 TYR cc_start: 0.8840 (t80) cc_final: 0.8619 (t80) REVERT: F 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8526 (mmt) REVERT: F 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8690 (tt) REVERT: F 186 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7758 (tp30) REVERT: F 233 MET cc_start: 0.9255 (mmm) cc_final: 0.9003 (mmm) REVERT: F 320 ILE cc_start: 0.8992 (mt) cc_final: 0.8791 (mt) REVERT: F 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7673 (tt0) REVERT: F 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6982 (t70) REVERT: F 1031 ASP cc_start: 0.8795 (m-30) cc_final: 0.8484 (p0) REVERT: F 1064 TYR cc_start: 0.7669 (m-80) cc_final: 0.7446 (m-80) REVERT: F 1168 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8039 (tp) REVERT: F 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8262 (pp) REVERT: F 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8781 (mmp80) REVERT: F 1252 MET cc_start: 0.9033 (ttm) cc_final: 0.8720 (mmt) REVERT: G 91 TRP cc_start: 0.9115 (t60) cc_final: 0.8848 (t-100) REVERT: G 131 ILE cc_start: 0.8714 (pt) cc_final: 0.8507 (mt) REVERT: G 152 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8625 (tp40) REVERT: G 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7256 (mtt180) REVERT: G 177 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: H 51 TRP cc_start: 0.7653 (t60) cc_final: 0.6546 (m-10) REVERT: H 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8665 (m-10) REVERT: H 136 LEU cc_start: 0.8062 (mt) cc_final: 0.7538 (pp) REVERT: H 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6642 (t80) REVERT: H 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8617 (t80) REVERT: H 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8524 (mmt) REVERT: H 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8691 (tt) REVERT: H 186 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7759 (tp30) REVERT: H 233 MET cc_start: 0.9257 (mmm) cc_final: 0.9004 (mmm) REVERT: H 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7674 (tt0) REVERT: H 570 ASP cc_start: 0.7534 (m-30) cc_final: 0.6977 (t70) REVERT: H 1031 ASP cc_start: 0.8798 (m-30) cc_final: 0.8484 (p0) REVERT: H 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7447 (m-80) REVERT: H 1168 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (tp) REVERT: H 1171 LEU cc_start: 0.8467 (mt) cc_final: 0.8263 (pp) REVERT: H 1246 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8782 (mmp80) REVERT: H 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8723 (mmt) outliers start: 248 outliers final: 48 residues processed: 1114 average time/residue: 0.1930 time to fit residues: 349.7383 Evaluate side-chains 525 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 465 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN B 326 HIS B 485 GLN B1020 GLN B1296 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 326 HIS D 485 GLN D1020 GLN D1296 ASN F 262 ASN F 326 HIS F 485 GLN F1020 GLN F1296 ASN H 262 ASN H 326 HIS H 485 GLN H1020 GLN H1296 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083081 restraints weight = 110301.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082621 restraints weight = 103745.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083257 restraints weight = 91660.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.083586 restraints weight = 65196.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083770 restraints weight = 59976.759| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31316 Z= 0.183 Angle : 0.694 8.001 42596 Z= 0.356 Chirality : 0.041 0.187 5196 Planarity : 0.005 0.061 5116 Dihedral : 5.871 62.173 4236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.76 % Rotamer: Outliers : 0.12 % Allowed : 3.77 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 3832 helix: 0.75 (0.09), residues: 3172 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1251 TYR 0.017 0.001 TYR B 512 PHE 0.026 0.002 PHE F 295 TRP 0.009 0.001 TRP B 75 HIS 0.005 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00360 (31312) covalent geometry : angle 0.69327 (42588) SS BOND : bond 0.00916 ( 4) SS BOND : angle 1.65710 ( 8) hydrogen bonds : bond 0.06821 ( 2472) hydrogen bonds : angle 4.59527 ( 7392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 633 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7853 (tptt) cc_final: 0.7040 (mptt) REVERT: A 54 ARG cc_start: 0.5226 (mtm-85) cc_final: 0.4873 (ptm160) REVERT: A 137 MET cc_start: 0.7904 (mmm) cc_final: 0.7192 (tmm) REVERT: A 154 ILE cc_start: 0.9477 (tp) cc_final: 0.9248 (tp) REVERT: B 51 TRP cc_start: 0.7340 (t60) cc_final: 0.6746 (m-10) REVERT: B 157 PHE cc_start: 0.5382 (t80) cc_final: 0.5174 (t80) REVERT: B 184 LEU cc_start: 0.9241 (mt) cc_final: 0.8682 (tt) REVERT: B 186 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7089 (tp30) REVERT: B 391 ILE cc_start: 0.9459 (pt) cc_final: 0.9254 (mt) REVERT: B 507 LYS cc_start: 0.8325 (tptt) cc_final: 0.7994 (mmtm) REVERT: B 1298 MET cc_start: 0.8337 (ttt) cc_final: 0.8078 (ttt) REVERT: C 54 ARG cc_start: 0.5233 (mtm-85) cc_final: 0.4883 (ptm160) REVERT: C 137 MET cc_start: 0.7891 (mmm) cc_final: 0.7226 (tmm) REVERT: D 51 TRP cc_start: 0.7347 (t60) cc_final: 0.6745 (m-10) REVERT: D 157 PHE cc_start: 0.5376 (t80) cc_final: 0.5142 (t80) REVERT: D 184 LEU cc_start: 0.9236 (mt) cc_final: 0.8685 (tt) REVERT: D 186 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7089 (tp30) REVERT: D 507 LYS cc_start: 0.8313 (tptt) cc_final: 0.7987 (mmtm) REVERT: D 1298 MET cc_start: 0.8323 (ttt) cc_final: 0.8060 (ttt) REVERT: E 54 ARG cc_start: 0.5229 (mtm-85) cc_final: 0.4867 (ptm160) REVERT: E 137 MET cc_start: 0.7999 (mmm) cc_final: 0.7255 (tmm) REVERT: F 51 TRP cc_start: 0.7349 (t60) cc_final: 0.6745 (m-10) REVERT: F 157 PHE cc_start: 0.5369 (t80) cc_final: 0.5157 (t80) REVERT: F 184 LEU cc_start: 0.9238 (mt) cc_final: 0.8680 (tt) REVERT: F 186 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7094 (tp30) REVERT: F 391 ILE cc_start: 0.9452 (pt) cc_final: 0.9251 (mt) REVERT: F 507 LYS cc_start: 0.8311 (tptt) cc_final: 0.7986 (mmtm) REVERT: F 1298 MET cc_start: 0.8322 (ttt) cc_final: 0.8051 (ttt) REVERT: G 54 ARG cc_start: 0.5247 (mtm-85) cc_final: 0.4883 (ptm160) REVERT: G 137 MET cc_start: 0.7982 (mmm) cc_final: 0.7391 (tmm) REVERT: H 51 TRP cc_start: 0.7340 (t60) cc_final: 0.6742 (m-10) REVERT: H 157 PHE cc_start: 0.5398 (t80) cc_final: 0.5164 (t80) REVERT: H 184 LEU cc_start: 0.9232 (mt) cc_final: 0.8681 (tt) REVERT: H 186 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7090 (tp30) REVERT: H 507 LYS cc_start: 0.8305 (tptt) cc_final: 0.7984 (mmtm) REVERT: H 1298 MET cc_start: 0.8339 (ttt) cc_final: 0.8077 (ttt) outliers start: 4 outliers final: 0 residues processed: 637 average time/residue: 0.1911 time to fit residues: 199.3169 Evaluate side-chains 382 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 157 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 359 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 262 ASN B 326 HIS B1020 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS D1020 GLN E 152 GLN F 262 ASN F1020 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079616 restraints weight = 110040.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079049 restraints weight = 99642.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079782 restraints weight = 95025.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079728 restraints weight = 70506.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079882 restraints weight = 59886.078| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31316 Z= 0.187 Angle : 0.683 8.176 42596 Z= 0.351 Chirality : 0.041 0.184 5196 Planarity : 0.005 0.055 5116 Dihedral : 5.445 55.878 4236 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3832 helix: 1.30 (0.09), residues: 3184 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F1251 TYR 0.017 0.001 TYR D 230 PHE 0.032 0.002 PHE D 295 TRP 0.037 0.002 TRP B1088 HIS 0.010 0.001 HIS H 71 Details of bonding type rmsd covalent geometry : bond 0.00397 (31312) covalent geometry : angle 0.68273 (42588) SS BOND : bond 0.00608 ( 4) SS BOND : angle 1.20585 ( 8) hydrogen bonds : bond 0.05960 ( 2472) hydrogen bonds : angle 4.23085 ( 7392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 511 time to evaluate : 1.154 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: A 47 LYS cc_start: 0.8262 (tptt) cc_final: 0.7410 (mptt) REVERT: A 54 ARG cc_start: 0.5714 (mtm-85) cc_final: 0.5163 (ptm160) REVERT: A 82 SER cc_start: 0.9386 (p) cc_final: 0.9123 (m) REVERT: A 118 SER cc_start: 0.9090 (m) cc_final: 0.8542 (t) REVERT: B 104 LEU cc_start: 0.8752 (mt) cc_final: 0.8322 (mt) REVERT: B 108 MET cc_start: 0.8027 (mmm) cc_final: 0.7827 (mpp) REVERT: B 136 LEU cc_start: 0.7426 (mt) cc_final: 0.7099 (pp) REVERT: B 157 PHE cc_start: 0.6037 (t80) cc_final: 0.5582 (t80) REVERT: B 184 LEU cc_start: 0.9208 (mt) cc_final: 0.8711 (tt) REVERT: B 186 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7051 (tp30) REVERT: B 326 HIS cc_start: 0.6800 (t70) cc_final: 0.6550 (t-170) REVERT: B 494 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: B 1031 ASP cc_start: 0.8472 (p0) cc_final: 0.8159 (p0) REVERT: B 1110 MET cc_start: 0.2462 (mmt) cc_final: 0.2034 (mmt) REVERT: C 54 ARG cc_start: 0.5722 (mtm-85) cc_final: 0.5225 (ptm160) REVERT: C 82 SER cc_start: 0.9374 (p) cc_final: 0.9122 (m) REVERT: C 159 ILE cc_start: 0.9232 (tp) cc_final: 0.9024 (tp) REVERT: C 168 PHE cc_start: 0.6851 (t80) cc_final: 0.6604 (t80) REVERT: D 104 LEU cc_start: 0.8747 (mt) cc_final: 0.8343 (mt) REVERT: D 136 LEU cc_start: 0.7371 (mt) cc_final: 0.7072 (pp) REVERT: D 157 PHE cc_start: 0.5998 (t80) cc_final: 0.5544 (t80) REVERT: D 184 LEU cc_start: 0.9204 (mt) cc_final: 0.8713 (tt) REVERT: D 186 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7032 (tp30) REVERT: D 326 HIS cc_start: 0.6807 (t70) cc_final: 0.6562 (t-170) REVERT: D 417 ILE cc_start: 0.9456 (mt) cc_final: 0.8993 (tp) REVERT: D 1031 ASP cc_start: 0.8479 (p0) cc_final: 0.8166 (p0) REVERT: D 1110 MET cc_start: 0.2517 (mmt) cc_final: 0.2078 (mmt) REVERT: E 54 ARG cc_start: 0.5703 (mtm-85) cc_final: 0.5173 (ptm160) REVERT: E 82 SER cc_start: 0.9362 (p) cc_final: 0.9120 (m) REVERT: E 118 SER cc_start: 0.9104 (m) cc_final: 0.8578 (t) REVERT: E 168 PHE cc_start: 0.6817 (t80) cc_final: 0.6168 (t80) REVERT: F 104 LEU cc_start: 0.8740 (mt) cc_final: 0.8344 (mt) REVERT: F 136 LEU cc_start: 0.7386 (mt) cc_final: 0.7076 (pp) REVERT: F 157 PHE cc_start: 0.6004 (t80) cc_final: 0.5553 (t80) REVERT: F 184 LEU cc_start: 0.9203 (mt) cc_final: 0.8702 (tt) REVERT: F 186 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7040 (tp30) REVERT: F 417 ILE cc_start: 0.9449 (mt) cc_final: 0.9001 (tp) REVERT: F 1031 ASP cc_start: 0.8480 (p0) cc_final: 0.8168 (p0) REVERT: F 1110 MET cc_start: 0.2486 (mmt) cc_final: 0.2050 (mmt) REVERT: G 54 ARG cc_start: 0.5732 (mtm-85) cc_final: 0.5217 (ptm160) REVERT: G 82 SER cc_start: 0.9377 (p) cc_final: 0.9101 (m) REVERT: H 104 LEU cc_start: 0.8750 (mt) cc_final: 0.8334 (mt) REVERT: H 136 LEU cc_start: 0.7418 (mt) cc_final: 0.7094 (pp) REVERT: H 157 PHE cc_start: 0.6013 (t80) cc_final: 0.5551 (t80) REVERT: H 184 LEU cc_start: 0.9205 (mt) cc_final: 0.8702 (tt) REVERT: H 186 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7029 (tp30) REVERT: H 1031 ASP cc_start: 0.8492 (p0) cc_final: 0.8177 (p0) REVERT: H 1110 MET cc_start: 0.2485 (mmt) cc_final: 0.2047 (mmt) outliers start: 4 outliers final: 0 residues processed: 515 average time/residue: 0.1726 time to fit residues: 150.9124 Evaluate side-chains 352 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 302 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 342 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 326 HIS ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 326 HIS ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.095847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079688 restraints weight = 110298.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079002 restraints weight = 103117.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079609 restraints weight = 87683.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080231 restraints weight = 61997.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.080398 restraints weight = 56197.548| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31316 Z= 0.160 Angle : 0.634 7.971 42596 Z= 0.322 Chirality : 0.039 0.166 5196 Planarity : 0.005 0.076 5116 Dihedral : 5.294 53.226 4236 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.14), residues: 3832 helix: 1.66 (0.09), residues: 3176 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.022 0.001 TYR D 123 PHE 0.040 0.002 PHE D 583 TRP 0.014 0.002 TRP E 90 HIS 0.008 0.001 HIS H 326 Details of bonding type rmsd covalent geometry : bond 0.00337 (31312) covalent geometry : angle 0.63347 (42588) SS BOND : bond 0.00814 ( 4) SS BOND : angle 1.33805 ( 8) hydrogen bonds : bond 0.05450 ( 2472) hydrogen bonds : angle 4.07838 ( 7392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8318 (tptt) cc_final: 0.7450 (mptt) REVERT: A 54 ARG cc_start: 0.5780 (mtm-85) cc_final: 0.5239 (ptm160) REVERT: A 82 SER cc_start: 0.9353 (p) cc_final: 0.9059 (m) REVERT: A 168 PHE cc_start: 0.7280 (t80) cc_final: 0.6861 (t80) REVERT: B 104 LEU cc_start: 0.8702 (mt) cc_final: 0.8379 (mt) REVERT: B 136 LEU cc_start: 0.7348 (mt) cc_final: 0.7035 (pp) REVERT: B 181 MET cc_start: 0.8887 (mmm) cc_final: 0.8484 (mmt) REVERT: B 184 LEU cc_start: 0.9206 (mt) cc_final: 0.8719 (tt) REVERT: B 507 LYS cc_start: 0.8574 (mmtm) cc_final: 0.7923 (mttp) REVERT: B 583 PHE cc_start: 0.9184 (m-80) cc_final: 0.8795 (m-80) REVERT: B 1298 MET cc_start: 0.8611 (ttt) cc_final: 0.8319 (ttt) REVERT: C 54 ARG cc_start: 0.5880 (mtm-85) cc_final: 0.5269 (ptm160) REVERT: C 82 SER cc_start: 0.9352 (p) cc_final: 0.9069 (m) REVERT: D 136 LEU cc_start: 0.7330 (mt) cc_final: 0.7031 (pp) REVERT: D 181 MET cc_start: 0.8879 (mmm) cc_final: 0.8486 (mmt) REVERT: D 184 LEU cc_start: 0.9209 (mt) cc_final: 0.8712 (tt) REVERT: D 507 LYS cc_start: 0.8555 (mmtm) cc_final: 0.7908 (mttp) REVERT: D 583 PHE cc_start: 0.9175 (m-80) cc_final: 0.8787 (m-80) REVERT: D 1298 MET cc_start: 0.8618 (ttt) cc_final: 0.8324 (ttt) REVERT: E 54 ARG cc_start: 0.5880 (mtm-85) cc_final: 0.5262 (ptm160) REVERT: E 82 SER cc_start: 0.9349 (p) cc_final: 0.9068 (m) REVERT: F 88 GLU cc_start: 0.8353 (tp30) cc_final: 0.8150 (tp30) REVERT: F 136 LEU cc_start: 0.7326 (mt) cc_final: 0.7036 (pp) REVERT: F 181 MET cc_start: 0.8876 (mmm) cc_final: 0.8478 (mmt) REVERT: F 184 LEU cc_start: 0.9199 (mt) cc_final: 0.8709 (tt) REVERT: F 507 LYS cc_start: 0.8570 (mmtm) cc_final: 0.7926 (mttp) REVERT: F 583 PHE cc_start: 0.9185 (m-80) cc_final: 0.8802 (m-80) REVERT: F 1298 MET cc_start: 0.8597 (ttt) cc_final: 0.8298 (ttt) REVERT: G 54 ARG cc_start: 0.5892 (mtm-85) cc_final: 0.5265 (ptm160) REVERT: G 82 SER cc_start: 0.9352 (p) cc_final: 0.9090 (m) REVERT: G 168 PHE cc_start: 0.7206 (t80) cc_final: 0.6946 (t80) REVERT: H 88 GLU cc_start: 0.8351 (tp30) cc_final: 0.8145 (tp30) REVERT: H 136 LEU cc_start: 0.7333 (mt) cc_final: 0.7030 (pp) REVERT: H 181 MET cc_start: 0.8887 (mmm) cc_final: 0.8494 (mmt) REVERT: H 184 LEU cc_start: 0.9213 (mt) cc_final: 0.8708 (tt) REVERT: H 507 LYS cc_start: 0.8562 (mmtm) cc_final: 0.7922 (mttp) REVERT: H 583 PHE cc_start: 0.9176 (m-80) cc_final: 0.8785 (m-80) REVERT: H 1298 MET cc_start: 0.8588 (ttt) cc_final: 0.8296 (ttt) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1726 time to fit residues: 137.3255 Evaluate side-chains 304 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 192 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D1020 GLN F 262 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079578 restraints weight = 110243.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.078651 restraints weight = 106979.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.079299 restraints weight = 96007.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079990 restraints weight = 66651.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.080192 restraints weight = 59379.054| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31316 Z= 0.157 Angle : 0.622 8.107 42596 Z= 0.317 Chirality : 0.038 0.178 5196 Planarity : 0.005 0.067 5116 Dihedral : 5.138 49.997 4236 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.14), residues: 3832 helix: 1.70 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -0.68 (0.30), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 136 TYR 0.017 0.001 TYR B 123 PHE 0.031 0.002 PHE F1113 TRP 0.011 0.001 TRP B1088 HIS 0.009 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00336 (31312) covalent geometry : angle 0.62200 (42588) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.22480 ( 8) hydrogen bonds : bond 0.05217 ( 2472) hydrogen bonds : angle 3.99956 ( 7392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8365 (tptt) cc_final: 0.7562 (mptt) REVERT: A 54 ARG cc_start: 0.6149 (mtm-85) cc_final: 0.5515 (ptm160) REVERT: B 184 LEU cc_start: 0.9223 (mt) cc_final: 0.8709 (tt) REVERT: C 54 ARG cc_start: 0.6159 (mtm-85) cc_final: 0.5423 (ptm160) REVERT: D 184 LEU cc_start: 0.9216 (mt) cc_final: 0.8706 (tt) REVERT: E 54 ARG cc_start: 0.6180 (mtm-85) cc_final: 0.5452 (ptm160) REVERT: E 82 SER cc_start: 0.9467 (p) cc_final: 0.9230 (m) REVERT: F 184 LEU cc_start: 0.9214 (mt) cc_final: 0.8701 (tt) REVERT: G 54 ARG cc_start: 0.6163 (mtm-85) cc_final: 0.5442 (ptm160) REVERT: H 184 LEU cc_start: 0.9211 (mt) cc_final: 0.8701 (tt) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 0.1735 time to fit residues: 133.0465 Evaluate side-chains 291 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 239 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B1135 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D1135 HIS F 262 ASN F1135 HIS ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1135 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078330 restraints weight = 110027.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077405 restraints weight = 109849.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077962 restraints weight = 99253.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078467 restraints weight = 66613.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.078746 restraints weight = 59522.679| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31316 Z= 0.174 Angle : 0.637 7.559 42596 Z= 0.326 Chirality : 0.039 0.198 5196 Planarity : 0.005 0.066 5116 Dihedral : 5.141 47.337 4236 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.14), residues: 3832 helix: 1.71 (0.09), residues: 3204 sheet: None (None), residues: 0 loop : -0.79 (0.29), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H1251 TYR 0.017 0.001 TYR F 124 PHE 0.045 0.002 PHE G 75 TRP 0.010 0.001 TRP F1037 HIS 0.009 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00378 (31312) covalent geometry : angle 0.63681 (42588) SS BOND : bond 0.01287 ( 4) SS BOND : angle 1.20994 ( 8) hydrogen bonds : bond 0.05138 ( 2472) hydrogen bonds : angle 4.04414 ( 7392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.162 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: A 47 LYS cc_start: 0.8418 (tptt) cc_final: 0.7601 (mptt) REVERT: A 54 ARG cc_start: 0.6354 (mtm-85) cc_final: 0.5551 (ptm160) REVERT: A 110 CYS cc_start: 0.6618 (m) cc_final: 0.6416 (m) REVERT: B 108 MET cc_start: 0.8156 (mmm) cc_final: 0.7868 (mpp) REVERT: B 184 LEU cc_start: 0.9300 (mt) cc_final: 0.8767 (tt) REVERT: B 423 ILE cc_start: 0.7909 (pt) cc_final: 0.7500 (mm) REVERT: B 507 LYS cc_start: 0.8571 (mmtm) cc_final: 0.7745 (mttp) REVERT: B 583 PHE cc_start: 0.9099 (m-80) cc_final: 0.8794 (m-80) REVERT: C 54 ARG cc_start: 0.6198 (mtm-85) cc_final: 0.5534 (ptm160) REVERT: C 110 CYS cc_start: 0.6582 (m) cc_final: 0.6360 (m) REVERT: D 184 LEU cc_start: 0.9299 (mt) cc_final: 0.8761 (tt) REVERT: D 507 LYS cc_start: 0.8582 (mmtm) cc_final: 0.7761 (mttp) REVERT: D 583 PHE cc_start: 0.9073 (m-80) cc_final: 0.8785 (m-80) REVERT: E 54 ARG cc_start: 0.6237 (mtm-85) cc_final: 0.5534 (ptm160) REVERT: E 82 SER cc_start: 0.9519 (p) cc_final: 0.9281 (m) REVERT: E 110 CYS cc_start: 0.6527 (m) cc_final: 0.6327 (m) REVERT: E 168 PHE cc_start: 0.6455 (t80) cc_final: 0.5516 (t80) REVERT: F 184 LEU cc_start: 0.9299 (mt) cc_final: 0.8762 (tt) REVERT: F 507 LYS cc_start: 0.8572 (mmtm) cc_final: 0.7754 (mttp) REVERT: F 583 PHE cc_start: 0.9090 (m-80) cc_final: 0.8833 (m-80) REVERT: G 54 ARG cc_start: 0.6233 (mtm-85) cc_final: 0.5546 (ptm160) REVERT: H 184 LEU cc_start: 0.9304 (mt) cc_final: 0.8765 (tt) REVERT: H 507 LYS cc_start: 0.8580 (mmtm) cc_final: 0.7764 (mttp) REVERT: H 583 PHE cc_start: 0.9088 (m-80) cc_final: 0.8797 (m-80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1686 time to fit residues: 119.2061 Evaluate side-chains 296 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 chunk 254 optimal weight: 0.0060 chunk 292 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN B1020 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN F 262 ASN F1020 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1020 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079595 restraints weight = 110422.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079352 restraints weight = 103920.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.079989 restraints weight = 89964.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080025 restraints weight = 63635.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.080611 restraints weight = 55852.448| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31316 Z= 0.142 Angle : 0.628 7.826 42596 Z= 0.313 Chirality : 0.038 0.145 5196 Planarity : 0.005 0.090 5116 Dihedral : 4.971 44.895 4236 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3832 helix: 1.83 (0.09), residues: 3204 sheet: None (None), residues: 0 loop : -0.74 (0.29), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H1251 TYR 0.015 0.001 TYR H 123 PHE 0.029 0.002 PHE A 168 TRP 0.011 0.001 TRP F1037 HIS 0.008 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00295 (31312) covalent geometry : angle 0.62789 (42588) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.43982 ( 8) hydrogen bonds : bond 0.04891 ( 2472) hydrogen bonds : angle 3.90746 ( 7392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8419 (tptt) cc_final: 0.7682 (mptt) REVERT: A 54 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.5598 (ptm160) REVERT: A 81 CYS cc_start: 0.8203 (t) cc_final: 0.7957 (t) REVERT: A 110 CYS cc_start: 0.6649 (m) cc_final: 0.6411 (m) REVERT: B 184 LEU cc_start: 0.9260 (mt) cc_final: 0.8742 (tt) REVERT: B 507 LYS cc_start: 0.8663 (mmtm) cc_final: 0.7924 (mttt) REVERT: B 583 PHE cc_start: 0.8972 (m-80) cc_final: 0.8734 (m-80) REVERT: C 54 ARG cc_start: 0.6308 (mtm-85) cc_final: 0.5511 (ptm160) REVERT: C 110 CYS cc_start: 0.6643 (m) cc_final: 0.6407 (m) REVERT: D 184 LEU cc_start: 0.9242 (mt) cc_final: 0.8729 (tt) REVERT: D 419 ASN cc_start: 0.8559 (m110) cc_final: 0.8214 (m110) REVERT: D 423 ILE cc_start: 0.7805 (pt) cc_final: 0.7475 (mm) REVERT: D 507 LYS cc_start: 0.8677 (mmtm) cc_final: 0.7938 (mttt) REVERT: D 583 PHE cc_start: 0.8962 (m-80) cc_final: 0.8739 (m-80) REVERT: E 54 ARG cc_start: 0.6335 (mtm-85) cc_final: 0.5489 (ptm160) REVERT: E 110 CYS cc_start: 0.6568 (m) cc_final: 0.6317 (m) REVERT: F 108 MET cc_start: 0.8090 (mmm) cc_final: 0.7867 (mpp) REVERT: F 184 LEU cc_start: 0.9240 (mt) cc_final: 0.8730 (tt) REVERT: F 419 ASN cc_start: 0.8589 (m110) cc_final: 0.8222 (m110) REVERT: F 423 ILE cc_start: 0.7787 (pt) cc_final: 0.7437 (mm) REVERT: F 507 LYS cc_start: 0.8666 (mmtm) cc_final: 0.7927 (mttt) REVERT: F 583 PHE cc_start: 0.8971 (m-80) cc_final: 0.8685 (m-80) REVERT: G 54 ARG cc_start: 0.6351 (mtm-85) cc_final: 0.5505 (ptm160) REVERT: G 81 CYS cc_start: 0.8172 (t) cc_final: 0.7950 (t) REVERT: G 91 TRP cc_start: 0.8962 (t60) cc_final: 0.8685 (t60) REVERT: H 108 MET cc_start: 0.8118 (mmm) cc_final: 0.7883 (mpp) REVERT: H 184 LEU cc_start: 0.9246 (mt) cc_final: 0.8731 (tt) REVERT: H 419 ASN cc_start: 0.8602 (m-40) cc_final: 0.8339 (m110) REVERT: H 423 ILE cc_start: 0.7844 (pt) cc_final: 0.7501 (mm) REVERT: H 507 LYS cc_start: 0.8678 (mmtm) cc_final: 0.7952 (mttt) REVERT: H 583 PHE cc_start: 0.8993 (m-80) cc_final: 0.8756 (m-80) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1665 time to fit residues: 125.9779 Evaluate side-chains 316 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 136 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 375 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN D 427 GLN F 427 GLN ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN H 427 GLN ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077241 restraints weight = 110074.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076453 restraints weight = 97895.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077091 restraints weight = 92880.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077123 restraints weight = 64935.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078291 restraints weight = 57068.806| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31316 Z= 0.198 Angle : 0.678 8.913 42596 Z= 0.345 Chirality : 0.040 0.205 5196 Planarity : 0.005 0.080 5116 Dihedral : 5.092 47.961 4236 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.14), residues: 3832 helix: 1.67 (0.09), residues: 3200 sheet: None (None), residues: 0 loop : -0.96 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H1251 TYR 0.027 0.002 TYR D 123 PHE 0.034 0.002 PHE E 168 TRP 0.012 0.001 TRP F 232 HIS 0.008 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00439 (31312) covalent geometry : angle 0.67784 (42588) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.49735 ( 8) hydrogen bonds : bond 0.05086 ( 2472) hydrogen bonds : angle 4.06580 ( 7392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8317 (tptt) cc_final: 0.7652 (mptt) REVERT: A 54 ARG cc_start: 0.6427 (mtm-85) cc_final: 0.5088 (ttm170) REVERT: A 65 ASP cc_start: 0.7054 (t0) cc_final: 0.6803 (t0) REVERT: A 81 CYS cc_start: 0.8131 (t) cc_final: 0.7902 (t) REVERT: A 110 CYS cc_start: 0.6473 (m) cc_final: 0.6272 (m) REVERT: B 184 LEU cc_start: 0.9268 (mt) cc_final: 0.8782 (tt) REVERT: B 507 LYS cc_start: 0.8689 (mmtm) cc_final: 0.7877 (mttp) REVERT: B 583 PHE cc_start: 0.9009 (m-80) cc_final: 0.8728 (m-80) REVERT: C 54 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.5099 (ttm170) REVERT: C 65 ASP cc_start: 0.7070 (t0) cc_final: 0.6796 (t0) REVERT: D 184 LEU cc_start: 0.9265 (mt) cc_final: 0.8767 (tt) REVERT: D 507 LYS cc_start: 0.8689 (mmtm) cc_final: 0.7878 (mttp) REVERT: D 583 PHE cc_start: 0.8977 (m-80) cc_final: 0.8723 (m-80) REVERT: E 54 ARG cc_start: 0.6429 (mtm-85) cc_final: 0.5106 (ttm170) REVERT: E 65 ASP cc_start: 0.7102 (t0) cc_final: 0.6831 (t0) REVERT: F 184 LEU cc_start: 0.9259 (mt) cc_final: 0.8764 (tt) REVERT: F 507 LYS cc_start: 0.8689 (mmtm) cc_final: 0.7882 (mttp) REVERT: G 54 ARG cc_start: 0.6436 (mtm-85) cc_final: 0.5104 (ttm170) REVERT: G 65 ASP cc_start: 0.7127 (t0) cc_final: 0.6852 (t0) REVERT: H 184 LEU cc_start: 0.9264 (mt) cc_final: 0.8762 (tt) REVERT: H 507 LYS cc_start: 0.8711 (mmtm) cc_final: 0.7910 (mttp) REVERT: H 583 PHE cc_start: 0.9026 (m-80) cc_final: 0.8777 (m-80) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1650 time to fit residues: 119.1825 Evaluate side-chains 284 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 287 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 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 = 0.3662 r_free = 0.3662 target = 0.093457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076841 restraints weight = 110831.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076566 restraints weight = 101053.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077124 restraints weight = 90992.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077228 restraints weight = 65613.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077721 restraints weight = 57408.290| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31316 Z= 0.179 Angle : 0.662 8.109 42596 Z= 0.337 Chirality : 0.039 0.205 5196 Planarity : 0.005 0.071 5116 Dihedral : 5.025 49.489 4236 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.14), residues: 3832 helix: 1.74 (0.09), residues: 3200 sheet: None (None), residues: 0 loop : -0.98 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1183 TYR 0.037 0.002 TYR B 123 PHE 0.035 0.002 PHE F 583 TRP 0.010 0.001 TRP D 232 HIS 0.008 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00397 (31312) covalent geometry : angle 0.66197 (42588) SS BOND : bond 0.00818 ( 4) SS BOND : angle 1.62479 ( 8) hydrogen bonds : bond 0.04998 ( 2472) hydrogen bonds : angle 4.03146 ( 7392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8328 (tptt) cc_final: 0.7717 (mptt) REVERT: A 54 ARG cc_start: 0.6364 (mtm-85) cc_final: 0.5044 (ttm170) REVERT: A 65 ASP cc_start: 0.7094 (t0) cc_final: 0.6829 (t0) REVERT: A 81 CYS cc_start: 0.8168 (t) cc_final: 0.7950 (t) REVERT: A 110 CYS cc_start: 0.6717 (m) cc_final: 0.6493 (m) REVERT: A 137 MET cc_start: 0.8334 (tpp) cc_final: 0.7926 (tpp) REVERT: B 184 LEU cc_start: 0.9254 (mt) cc_final: 0.8788 (tt) REVERT: B 507 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8214 (tppt) REVERT: B 583 PHE cc_start: 0.8916 (m-80) cc_final: 0.8713 (m-80) REVERT: C 54 ARG cc_start: 0.6439 (mtm-85) cc_final: 0.5110 (ttm170) REVERT: C 65 ASP cc_start: 0.7072 (t0) cc_final: 0.6819 (t0) REVERT: C 77 MET cc_start: 0.7882 (tmm) cc_final: 0.7663 (tmm) REVERT: D 184 LEU cc_start: 0.9235 (mt) cc_final: 0.8770 (tt) REVERT: D 507 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8190 (tppt) REVERT: E 54 ARG cc_start: 0.6482 (mtm-85) cc_final: 0.5134 (ttm170) REVERT: E 60 PHE cc_start: 0.7637 (m-80) cc_final: 0.7306 (m-80) REVERT: F 184 LEU cc_start: 0.9277 (mt) cc_final: 0.8776 (tt) REVERT: F 507 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8209 (tppt) REVERT: G 54 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.5085 (ttm170) REVERT: G 81 CYS cc_start: 0.8160 (t) cc_final: 0.7940 (t) REVERT: H 184 LEU cc_start: 0.9228 (mt) cc_final: 0.8774 (tt) REVERT: H 507 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8221 (tppt) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1663 time to fit residues: 115.4339 Evaluate side-chains 275 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 349 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 189 optimal weight: 0.0050 chunk 277 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1020 GLN B1098 HIS B1179 GLN ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1020 GLN ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1179 GLN H1020 GLN H1098 HIS H1179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.095508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079339 restraints weight = 108812.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080184 restraints weight = 98259.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080159 restraints weight = 85524.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080337 restraints weight = 57870.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080736 restraints weight = 50177.951| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31316 Z= 0.142 Angle : 0.668 14.974 42596 Z= 0.333 Chirality : 0.039 0.233 5196 Planarity : 0.005 0.069 5116 Dihedral : 4.907 49.481 4236 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.14), residues: 3832 helix: 1.74 (0.09), residues: 3220 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 176 TYR 0.036 0.001 TYR B 123 PHE 0.056 0.002 PHE F 583 TRP 0.011 0.001 TRP F1037 HIS 0.009 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00292 (31312) covalent geometry : angle 0.66754 (42588) SS BOND : bond 0.00330 ( 4) SS BOND : angle 1.56781 ( 8) hydrogen bonds : bond 0.04814 ( 2472) hydrogen bonds : angle 3.95635 ( 7392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8362 (tptt) cc_final: 0.7749 (mptt) REVERT: A 54 ARG cc_start: 0.6382 (mtm-85) cc_final: 0.5107 (ttm170) REVERT: A 110 CYS cc_start: 0.6730 (m) cc_final: 0.6492 (m) REVERT: B 184 LEU cc_start: 0.9247 (mt) cc_final: 0.8747 (tt) REVERT: B 507 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8069 (tppt) REVERT: B 530 MET cc_start: 0.8400 (mpp) cc_final: 0.8113 (mmt) REVERT: C 54 ARG cc_start: 0.6211 (mtm-85) cc_final: 0.4969 (ttm170) REVERT: C 77 MET cc_start: 0.8015 (tmm) cc_final: 0.7777 (tmm) REVERT: D 184 LEU cc_start: 0.9229 (mt) cc_final: 0.8746 (tt) REVERT: D 507 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8073 (tppt) REVERT: D 530 MET cc_start: 0.8379 (mpp) cc_final: 0.8124 (mmt) REVERT: D 583 PHE cc_start: 0.8875 (m-80) cc_final: 0.8668 (m-80) REVERT: D 1298 MET cc_start: 0.8344 (ttt) cc_final: 0.8143 (ttt) REVERT: E 54 ARG cc_start: 0.6312 (mtm-85) cc_final: 0.4990 (ttm170) REVERT: F 184 LEU cc_start: 0.9275 (mt) cc_final: 0.8744 (tt) REVERT: F 507 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8075 (tppt) REVERT: F 530 MET cc_start: 0.8384 (mpp) cc_final: 0.8132 (mmt) REVERT: F 583 PHE cc_start: 0.8840 (m-80) cc_final: 0.8567 (m-80) REVERT: G 54 ARG cc_start: 0.6379 (mtm-85) cc_final: 0.5127 (ttm170) REVERT: H 184 LEU cc_start: 0.9231 (mt) cc_final: 0.8742 (tt) REVERT: H 507 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8095 (tppt) REVERT: H 530 MET cc_start: 0.8368 (mpp) cc_final: 0.8107 (mmt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1683 time to fit residues: 126.4296 Evaluate side-chains 275 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 352 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.093843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077460 restraints weight = 110824.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077190 restraints weight = 102273.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077764 restraints weight = 91852.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077935 restraints weight = 64374.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078341 restraints weight = 56377.373| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31316 Z= 0.184 Angle : 0.676 8.231 42596 Z= 0.345 Chirality : 0.040 0.207 5196 Planarity : 0.005 0.067 5116 Dihedral : 4.953 51.745 4236 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.14), residues: 3832 helix: 1.72 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 176 TYR 0.043 0.002 TYR F 123 PHE 0.054 0.002 PHE F 583 TRP 0.012 0.001 TRP D 232 HIS 0.008 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00411 (31312) covalent geometry : angle 0.67610 (42588) SS BOND : bond 0.00439 ( 4) SS BOND : angle 1.47146 ( 8) hydrogen bonds : bond 0.04911 ( 2472) hydrogen bonds : angle 4.04175 ( 7392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4503.10 seconds wall clock time: 79 minutes 9.51 seconds (4749.51 seconds total)