Starting phenix.real_space_refine on Sat Aug 8 05:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1h_65540/08_2026/9w1h_65540_trim.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 30 5.49 5 Mg 6 5.21 5 S 104 5.16 5 C 16000 2.51 5 N 4654 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25461 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 4645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4645 Classifications: {'peptide': 593} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 551} Chain breaks: 2 Chain: "D" Number of atoms: 4772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4772 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 568} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4775 Classifications: {'peptide': 610} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 568} Chain: "E" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3015 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 359} Chain: "F" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3035 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 363} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Chain: "Y" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4757 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 567} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.98, per 1000 atoms: 0.23 Number of scatterers: 25461 At special positions: 0 Unit cell: (96.928, 149.12, 219.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 104 16.00 P 30 15.00 Mg 6 11.99 O 4661 8.00 N 4654 7.00 C 16000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 461 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 262 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 260 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 260 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 262 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 461 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 262 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 461 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 260 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 260 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 262 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 461 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 260 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 461 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 260 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 461 " 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 11 sheets defined 52.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.641A pdb=" N GLN C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 73 through 91 Processing helix chain 'C' and resid 105 through 120 Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 167 through 172 removed outlier: 4.024A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 196 through 216 removed outlier: 3.529A pdb=" N ALA C 215 " --> pdb=" O HIS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.501A pdb=" N GLU C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.925A pdb=" N LEU C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 305 through 313 removed outlier: 4.128A pdb=" N ARG C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 342 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 382 through 386 Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 448 through 454 removed outlier: 3.518A pdb=" N VAL C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 477 removed outlier: 3.642A pdb=" N ILE C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 509 through 517 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.028A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'D' and resid 13 through 20 removed outlier: 3.637A pdb=" N GLN D 20 " --> pdb=" O PRO D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 4.109A pdb=" N GLY D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 91 removed outlier: 3.595A pdb=" N HIS D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 197 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.546A pdb=" N ALA D 229 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.509A pdb=" N HIS D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.098A pdb=" N ARG D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 342 Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 362 through 380 Processing helix chain 'D' and resid 403 through 420 removed outlier: 3.660A pdb=" N GLU D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 467 through 477 removed outlier: 4.205A pdb=" N ILE D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 491 removed outlier: 3.609A pdb=" N ARG D 491 " --> pdb=" O HIS D 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.534A pdb=" N THR D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 removed outlier: 3.515A pdb=" N GLN D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 602 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 20 through 21 No H-bonds generated for 'chain 'A' and resid 20 through 21' Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.991A pdb=" N GLN A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 26 " --> pdb=" O GLY A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 26' Processing helix chain 'A' and resid 39 through 54 removed outlier: 4.147A pdb=" N GLY A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.909A pdb=" N MET A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.762A pdb=" N ALA A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 Processing helix chain 'A' and resid 216 through 222 removed outlier: 4.124A pdb=" N SER A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.621A pdb=" N ALA A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.512A pdb=" N HIS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.826A pdb=" N LYS A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.562A pdb=" N THR A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.349A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.700A pdb=" N PHE A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Proline residue: A 450 - end of helix removed outlier: 3.519A pdb=" N VAL A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.788A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.653A pdb=" N THR A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.585A pdb=" N HIS E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 254 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.696A pdb=" N HIS E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 306 through 313 Processing helix chain 'E' and resid 320 through 323 removed outlier: 3.781A pdb=" N LYS E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 320 through 323' Processing helix chain 'E' and resid 324 through 342 Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 362 through 380 Processing helix chain 'E' and resid 381 through 386 removed outlier: 6.170A pdb=" N ASP E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 420 Processing helix chain 'E' and resid 432 through 435 removed outlier: 3.986A pdb=" N GLU E 435 " --> pdb=" O ALA E 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.550A pdb=" N ALA E 442 " --> pdb=" O THR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 540 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.125A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 Processing helix chain 'E' and resid 590 through 602 Processing helix chain 'F' and resid 224 through 230 removed outlier: 3.627A pdb=" N ALA F 228 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 229 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.880A pdb=" N LEU F 273 " --> pdb=" O HIS F 269 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.987A pdb=" N ARG F 309 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.688A pdb=" N LYS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 362 through 381 Processing helix chain 'F' and resid 382 through 386 removed outlier: 3.562A pdb=" N ARG F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 420 removed outlier: 3.554A pdb=" N ALA F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 435 removed outlier: 3.887A pdb=" N GLU F 435 " --> pdb=" O ALA F 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 432 through 435' Processing helix chain 'F' and resid 436 through 446 Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 556 through 568 removed outlier: 4.726A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 590 through 602 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 20 through 21 No H-bonds generated for 'chain 'B' and resid 20 through 21' Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.547A pdb=" N GLN B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 26 " --> pdb=" O GLY B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 26' Processing helix chain 'B' and resid 40 through 54 removed outlier: 3.590A pdb=" N ARG B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.548A pdb=" N HIS B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.518A pdb=" N ALA B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.519A pdb=" N HIS B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 326 through 327 No H-bonds generated for 'chain 'B' and resid 326 through 327' Processing helix chain 'B' and resid 329 through 329 No H-bonds generated for 'chain 'B' and resid 329 through 329' Processing helix chain 'B' and resid 330 through 342 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 404 through 420 removed outlier: 4.093A pdb=" N GLU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 4.752A pdb=" N PHE B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.594A pdb=" N THR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 590 through 602 Processing sheet with id=AA1, first strand: chain 'C' and resid 156 through 164 removed outlier: 6.779A pdb=" N LEU C 156 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 129 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 158 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 127 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG C 160 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE C 125 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY C 162 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU C 123 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 99 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 127 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER C 7 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU C 4 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU C 33 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS C 6 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 30 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER C 62 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 32 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL C 64 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 34 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N HIS C 189 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 61 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL C 191 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG C 63 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 256 through 262 removed outlier: 4.504A pdb=" N VAL C 257 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU C 348 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU C 259 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG C 350 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS C 261 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C 426 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 391 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 428 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 457 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C 483 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 157 through 164 removed outlier: 6.551A pdb=" N VAL D 124 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS D 122 " --> pdb=" O PRO D 163 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ARG D 97 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE D 125 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 99 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 127 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 7 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 30 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N SER D 62 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 32 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL D 64 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 34 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 262 removed outlier: 6.020A pdb=" N LYS D 256 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 346 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS D 260 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG D 350 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS D 262 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 426 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU D 391 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 428 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL D 427 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR D 459 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 429 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS D 461 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 431 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 483 " --> pdb=" O GLU D 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.342A pdb=" N SER A 7 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N HIS A 189 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 61 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 191 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 63 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 262 removed outlier: 6.090A pdb=" N LYS A 256 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 346 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS A 260 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG A 350 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS A 262 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 426 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 391 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 428 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 256 through 257 removed outlier: 7.425A pdb=" N LYS E 256 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA E 347 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS E 261 " --> pdb=" O ARG E 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 256 through 257 removed outlier: 7.425A pdb=" N LYS E 256 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA E 347 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 345 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ASN E 390 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA E 347 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU E 392 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 349 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR E 394 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS E 351 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 11.830A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 256 through 262 removed outlier: 4.535A pdb=" N VAL F 257 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU F 348 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 259 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG F 350 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS F 261 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N VAL F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N GLY F 428 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU F 391 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP F 430 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU F 393 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU F 483 " --> pdb=" O GLU F 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 160 removed outlier: 3.565A pdb=" N GLU B 123 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 30 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N HIS B 189 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 61 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 191 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG B 63 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 262 removed outlier: 7.295A pdb=" N LYS B 256 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA B 347 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 258 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE B 349 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N HIS B 260 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N CYS B 351 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N HIS B 262 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 388 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 426 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 391 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B 428 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3252 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: 5.30 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5052 1.33 - 1.45: 6163 1.45 - 1.57: 14707 1.57 - 1.69: 52 1.69 - 1.81: 144 Bond restraints: 26118 Sorted by residual: bond pdb=" CA SER C 37 " pdb=" CB SER C 37 " ideal model delta sigma weight residual 1.530 1.467 0.062 1.48e-02 4.57e+03 1.78e+01 bond pdb=" CA ALA B 215 " pdb=" CB ALA B 215 " ideal model delta sigma weight residual 1.536 1.481 0.056 1.58e-02 4.01e+03 1.24e+01 bond pdb=" CA ALA C 215 " pdb=" CB ALA C 215 " ideal model delta sigma weight residual 1.535 1.482 0.053 1.51e-02 4.39e+03 1.22e+01 bond pdb=" CA SER F 553 " pdb=" CB SER F 553 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.71e-02 3.42e+03 1.07e+01 bond pdb=" CA SER D 220 " pdb=" CB SER D 220 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.74e-02 3.30e+03 9.95e+00 ... (remaining 26113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 35365 2.66 - 5.32: 305 5.32 - 7.98: 23 7.98 - 10.64: 1 10.64 - 13.30: 2 Bond angle restraints: 35696 Sorted by residual: angle pdb=" N THR C 35 " pdb=" CA THR C 35 " pdb=" C THR C 35 " ideal model delta sigma weight residual 112.68 125.98 -13.30 1.33e+00 5.65e-01 1.00e+02 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 133.12 6.75 1.00e+00 1.00e+00 4.55e+01 angle pdb=" C THR C 35 " pdb=" CA THR C 35 " pdb=" CB THR C 35 " ideal model delta sigma weight residual 110.24 99.07 11.17 1.67e+00 3.59e-01 4.47e+01 angle pdb=" O5' A X 2 " pdb=" C5' A X 2 " pdb=" C4' A X 2 " ideal model delta sigma weight residual 109.40 113.38 -3.98 8.00e-01 1.56e+00 2.48e+01 angle pdb=" N ILE D 219 " pdb=" CA ILE D 219 " pdb=" C ILE D 219 " ideal model delta sigma weight residual 112.98 107.29 5.69 1.25e+00 6.40e-01 2.07e+01 ... (remaining 35691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.35: 14138 18.35 - 36.69: 1180 36.69 - 55.04: 324 55.04 - 73.38: 104 73.38 - 91.73: 18 Dihedral angle restraints: 15764 sinusoidal: 6517 harmonic: 9247 Sorted by residual: dihedral pdb=" CA GLN C 65 " pdb=" C GLN C 65 " pdb=" N ASP C 66 " pdb=" CA ASP C 66 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ILE C 40 " pdb=" C ILE C 40 " pdb=" N SER C 41 " pdb=" CA SER C 41 " ideal model delta harmonic sigma weight residual 180.00 -159.68 -20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN C 138 " pdb=" C ASN C 138 " pdb=" N ARG C 139 " pdb=" CA ARG C 139 " ideal model delta harmonic sigma weight residual 180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 15761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3647 0.081 - 0.161: 292 0.161 - 0.242: 10 0.242 - 0.322: 11 0.322 - 0.403: 1 Chirality restraints: 3961 Sorted by residual: chirality pdb=" CA ALA C 36 " pdb=" N ALA C 36 " pdb=" C ALA C 36 " pdb=" CB ALA C 36 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR C 35 " pdb=" N THR C 35 " pdb=" C THR C 35 " pdb=" CB THR C 35 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3958 not shown) Planarity restraints: 4622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 213 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C LEU D 213 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU D 213 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA D 214 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 219 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE B 219 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 219 " 0.016 2.00e-02 2.50e+03 pdb=" N SER B 220 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 41 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO C 42 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " -0.032 5.00e-02 4.00e+02 ... (remaining 4619 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 249 2.55 - 3.14: 20515 3.14 - 3.73: 40869 3.73 - 4.31: 57246 4.31 - 4.90: 96612 Nonbonded interactions: 215491 Sorted by model distance: nonbonded pdb=" OD1 ASP A 548 " pdb="ZN ZN A 702 " model vdw 1.967 2.230 nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 702 " model vdw 2.004 2.230 nonbonded pdb=" OD1 ASP C 548 " pdb="ZN ZN C 702 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASP D 548 " pdb="ZN ZN D 702 " model vdw 2.009 2.230 nonbonded pdb=" OD1 ASP E 548 " pdb="ZN ZN E 702 " model vdw 2.014 2.230 ... (remaining 215486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 327 or resid 329 through 396 or (re \ sid 397 through 398 and (name N or name CA or name C or name O or name CB )) or \ resid 402 through 433 or resid 446 through 608 or resid 701 through 703)) selection = (chain 'B' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 398 or resid 402 through 433 or res \ id 446 through 608 or resid 701 through 703)) selection = (chain 'C' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 327 or resid 329 through 396 or (re \ sid 397 through 398 and (name N or name CA or name C or name O or name CB )) or \ resid 402 through 703)) selection = (chain 'D' and (resid 1 through 327 or resid 329 through 396 or (resid 397 throu \ gh 398 and (name N or name CA or name C or name O or name CB )) or resid 402 thr \ ough 433 or resid 446 through 608 or resid 701 through 703)) } ncs_group { reference = (chain 'E' and (resid 220 through 396 or (resid 397 through 398 and (name N or n \ ame CA or name C or name O or name CB )) or resid 399 through 703)) selection = (chain 'F' and (resid 220 through 607 or resid 701 through 703)) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26136 Z= 0.209 Angle : 0.586 13.301 35696 Z= 0.328 Chirality : 0.045 0.403 3961 Planarity : 0.005 0.058 4622 Dihedral : 15.429 91.728 9764 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 2.72 % Allowed : 12.00 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: -0.01 (0.15), residues: 3184 helix: 0.97 (0.14), residues: 1437 sheet: -0.96 (0.26), residues: 442 loop : -0.67 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.015 0.001 TYR A 98 PHE 0.018 0.001 PHE C 67 TRP 0.022 0.002 TRP D 167 HIS 0.004 0.001 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (26118) covalent geometry : angle 0.58611 / 0.33 (35696) hydrogen bonds : bond 0.19492 / 12.92 ( 1160) hydrogen bonds : angle 6.50687 / 4.67 ( 3252) metal coordination : bond 0.01064 / 0.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 609 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8259 (tt0) cc_final: 0.7822 (tm-30) REVERT: C 198 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 203 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 207 GLU cc_start: 0.8595 (tp30) cc_final: 0.8217 (mp0) REVERT: C 601 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 71 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7628 (mpp-170) REVERT: D 203 GLU cc_start: 0.8496 (tp30) cc_final: 0.7960 (tp30) REVERT: D 208 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8459 (mtp180) REVERT: D 221 GLU cc_start: 0.8377 (pp20) cc_final: 0.8036 (tm-30) REVERT: D 308 GLU cc_start: 0.8035 (pm20) cc_final: 0.7809 (pm20) REVERT: D 383 GLU cc_start: 0.8210 (tp30) cc_final: 0.7862 (tp30) REVERT: D 526 GLU cc_start: 0.8443 (mp0) cc_final: 0.8171 (mp0) REVERT: D 575 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: A 25 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 52 GLU cc_start: 0.8205 (mp0) cc_final: 0.7842 (mp0) REVERT: A 96 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7451 (m170) REVERT: A 112 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8478 (mmt) REVERT: A 130 GLU cc_start: 0.7759 (tt0) cc_final: 0.7549 (tt0) REVERT: A 142 SER cc_start: 0.8821 (t) cc_final: 0.8511 (m) REVERT: A 181 GLU cc_start: 0.8341 (tt0) cc_final: 0.8129 (tt0) REVERT: A 185 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 221 GLU cc_start: 0.8351 (pp20) cc_final: 0.8071 (pp20) REVERT: A 236 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7591 (mtm180) REVERT: A 243 ASP cc_start: 0.8071 (t0) cc_final: 0.7727 (t0) REVERT: A 307 LEU cc_start: 0.8654 (tp) cc_final: 0.8365 (tm) REVERT: A 530 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8592 (p) REVERT: E 237 TRP cc_start: 0.8620 (t60) cc_final: 0.7874 (t60) REVERT: E 290 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.8206 (ttm110) REVERT: E 342 ASP cc_start: 0.8571 (t0) cc_final: 0.8303 (t0) REVERT: E 430 ASP cc_start: 0.8366 (t0) cc_final: 0.7674 (t0) REVERT: E 449 GLU cc_start: 0.8750 (tp30) cc_final: 0.8262 (tp30) REVERT: E 461 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8016 (m90) REVERT: E 600 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8383 (ttt90) REVERT: F 237 TRP cc_start: 0.8247 (t-100) cc_final: 0.7691 (t-100) REVERT: F 271 GLU cc_start: 0.7765 (tp30) cc_final: 0.7103 (tp30) REVERT: F 275 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8408 (ttmm) REVERT: F 279 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7987 (mm-30) REVERT: F 312 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7576 (mmp80) REVERT: F 315 ASP cc_start: 0.8810 (m-30) cc_final: 0.8502 (m-30) REVERT: F 348 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7963 (tt0) REVERT: F 383 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7497 (tm-30) REVERT: F 507 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8436 (mp0) REVERT: F 525 GLN cc_start: 0.8006 (pm20) cc_final: 0.7542 (pm20) REVERT: F 526 GLU cc_start: 0.8029 (tt0) cc_final: 0.7812 (tt0) REVERT: F 534 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8234 (mtt-85) REVERT: F 575 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7308 (mt-10) REVERT: B 96 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7671 (p90) REVERT: B 154 ASN cc_start: 0.8521 (t0) cc_final: 0.8262 (t0) REVERT: B 243 ASP cc_start: 0.8183 (p0) cc_final: 0.7784 (p0) REVERT: B 247 ASP cc_start: 0.8237 (m-30) cc_final: 0.7935 (m-30) REVERT: B 271 GLU cc_start: 0.8349 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 278 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7868 (tm130) REVERT: B 308 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7636 (pm20) REVERT: B 358 SER cc_start: 0.8957 (t) cc_final: 0.8691 (p) REVERT: B 430 ASP cc_start: 0.8232 (t0) cc_final: 0.7922 (t0) REVERT: B 449 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7971 (mm-30) outliers start: 71 outliers final: 31 residues processed: 657 average time/residue: 0.8955 time to fit residues: 657.5034 Evaluate side-chains 593 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 553 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 278 GLN C 390 ASN C 461 HIS C 513 ASN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 154 ASN D 278 GLN D 485 HIS D 546 ASN A 20 GLN A 76 HIS A 89 GLN A 488 HIS E 269 HIS E 372 ASN E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 546 ASN F 234 HIS F 422 ASN F 473 GLN F 603 GLN B 20 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN B 390 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097192 restraints weight = 45630.421| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 26136 Z= 0.152 Angle : 0.618 12.306 35696 Z= 0.313 Chirality : 0.042 0.148 3961 Planarity : 0.005 0.051 4622 Dihedral : 10.374 89.144 3915 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.53 % Allowed : 17.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.40 (0.16), residues: 3184 helix: 1.41 (0.14), residues: 1470 sheet: -0.96 (0.25), residues: 444 loop : -0.55 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 385 TYR 0.008 0.001 TYR B 98 PHE 0.014 0.001 PHE C 59 TRP 0.013 0.001 TRP D 167 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (26118) covalent geometry : angle 0.61796 / 0.31 (35696) hydrogen bonds : bond 0.04905 / 3.26 ( 1160) hydrogen bonds : angle 5.09165 / 3.70 ( 3252) metal coordination : bond 0.04532 / 2.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 584 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: C 157 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7821 (mtm180) REVERT: C 408 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7946 (mtt90) REVERT: C 453 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8362 (mmt90) REVERT: C 601 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 71 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: D 157 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7932 (ttm110) REVERT: D 203 GLU cc_start: 0.8417 (tp30) cc_final: 0.7808 (tp30) REVERT: D 221 GLU cc_start: 0.8440 (pp20) cc_final: 0.8010 (tm-30) REVERT: D 383 GLU cc_start: 0.8258 (tp30) cc_final: 0.8022 (mm-30) REVERT: D 443 MET cc_start: 0.7648 (mmm) cc_final: 0.7419 (mmm) REVERT: D 575 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 25 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8088 (mm-40) REVERT: A 29 GLU cc_start: 0.8220 (tt0) cc_final: 0.7465 (mt-10) REVERT: A 58 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7859 (mpp80) REVERT: A 74 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 136 GLN cc_start: 0.8506 (tt0) cc_final: 0.8055 (tm-30) REVERT: A 140 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5975 (mm-30) REVERT: A 142 SER cc_start: 0.8598 (t) cc_final: 0.8299 (p) REVERT: A 157 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8560 (mtm-85) REVERT: A 181 GLU cc_start: 0.8295 (tt0) cc_final: 0.8046 (tt0) REVERT: A 185 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 221 GLU cc_start: 0.8155 (pp20) cc_final: 0.7910 (pp20) REVERT: A 236 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7624 (mtm180) REVERT: A 243 ASP cc_start: 0.8397 (t0) cc_final: 0.8054 (t0) REVERT: A 307 LEU cc_start: 0.8522 (tp) cc_final: 0.8227 (tm) REVERT: A 530 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 237 TRP cc_start: 0.8638 (t60) cc_final: 0.7910 (t60) REVERT: E 248 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8096 (ttmm) REVERT: E 290 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8171 (ttm110) REVERT: E 312 ARG cc_start: 0.8216 (mmp-170) cc_final: 0.8008 (mmp80) REVERT: E 324 ASP cc_start: 0.8143 (t0) cc_final: 0.7851 (t0) REVERT: E 342 ASP cc_start: 0.8661 (t0) cc_final: 0.8380 (t0) REVERT: E 449 GLU cc_start: 0.8655 (tp30) cc_final: 0.8119 (tp30) REVERT: E 600 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8280 (ttt90) REVERT: F 237 TRP cc_start: 0.8307 (t-100) cc_final: 0.7722 (t-100) REVERT: F 271 GLU cc_start: 0.7630 (tp30) cc_final: 0.6970 (tp30) REVERT: F 275 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8427 (ttmm) REVERT: F 312 ARG cc_start: 0.7938 (mmp80) cc_final: 0.7543 (mmp80) REVERT: F 315 ASP cc_start: 0.8776 (m-30) cc_final: 0.8399 (m-30) REVERT: F 324 ASP cc_start: 0.8195 (t0) cc_final: 0.7841 (t70) REVERT: F 329 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8066 (ttm-80) REVERT: F 348 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: F 383 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 418 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8103 (mt-10) REVERT: F 491 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8059 (mtt-85) REVERT: F 507 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8429 (mt-10) REVERT: F 523 GLU cc_start: 0.7895 (tp30) cc_final: 0.7640 (tp30) REVERT: F 525 GLN cc_start: 0.7784 (pm20) cc_final: 0.7498 (pm20) REVERT: F 534 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8250 (mtt-85) REVERT: F 575 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 71 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7653 (mmm160) REVERT: B 145 GLU cc_start: 0.8621 (mp0) cc_final: 0.8385 (pm20) REVERT: B 154 ASN cc_start: 0.8568 (t0) cc_final: 0.8279 (t0) REVERT: B 184 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8386 (tp) REVERT: B 271 GLU cc_start: 0.8321 (tt0) cc_final: 0.7815 (tm-30) REVERT: B 278 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 308 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7622 (pm20) REVERT: B 324 ASP cc_start: 0.8507 (t0) cc_final: 0.8296 (t0) REVERT: B 358 SER cc_start: 0.8945 (t) cc_final: 0.8657 (p) REVERT: B 430 ASP cc_start: 0.8375 (t0) cc_final: 0.8164 (t0) REVERT: B 449 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8099 (mm-30) outliers start: 92 outliers final: 44 residues processed: 628 average time/residue: 0.9221 time to fit residues: 644.7756 Evaluate side-chains 612 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 557 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 329 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 252 GLN C 282 ASN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 546 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS A 488 HIS E 269 HIS E 375 GLN E 376 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS F 269 HIS F 422 ASN F 515 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096707 restraints weight = 46246.782| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.23 r_work: 0.3151 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26136 Z= 0.165 Angle : 0.590 7.665 35696 Z= 0.299 Chirality : 0.042 0.148 3961 Planarity : 0.005 0.050 4622 Dihedral : 9.931 89.443 3883 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.45 % Allowed : 18.79 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.48 (0.16), residues: 3184 helix: 1.50 (0.14), residues: 1470 sheet: -0.92 (0.25), residues: 445 loop : -0.54 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 49 TYR 0.009 0.001 TYR C 356 PHE 0.023 0.001 PHE A 51 TRP 0.015 0.001 TRP D 167 HIS 0.007 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (26118) covalent geometry : angle 0.59040 / 0.30 (35696) hydrogen bonds : bond 0.04385 / 2.92 ( 1160) hydrogen bonds : angle 4.80467 / 3.49 ( 3252) metal coordination : bond 0.00481 / 0.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 574 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7654 (mpp) cc_final: 0.7422 (mpp) REVERT: C 69 ASP cc_start: 0.8205 (p0) cc_final: 0.7843 (p0) REVERT: C 71 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7527 (ptp90) REVERT: C 132 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8156 (ptp90) REVERT: C 408 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7939 (mtt90) REVERT: C 601 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8398 (mp) REVERT: D 71 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: D 157 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7792 (ttm110) REVERT: D 203 GLU cc_start: 0.8373 (tp30) cc_final: 0.7759 (tp30) REVERT: D 221 GLU cc_start: 0.8471 (pp20) cc_final: 0.8038 (tm-30) REVERT: D 383 GLU cc_start: 0.8256 (tp30) cc_final: 0.8012 (mm-30) REVERT: D 397 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7612 (mtt180) REVERT: D 443 MET cc_start: 0.7684 (mmm) cc_final: 0.7419 (mmm) REVERT: A 25 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8120 (mm-40) REVERT: A 29 GLU cc_start: 0.8154 (tt0) cc_final: 0.7258 (mt-10) REVERT: A 58 ARG cc_start: 0.8268 (mtt180) cc_final: 0.7860 (mpp80) REVERT: A 74 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 130 GLU cc_start: 0.7716 (tt0) cc_final: 0.7451 (pt0) REVERT: A 140 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5829 (mt-10) REVERT: A 157 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8498 (mtm-85) REVERT: A 181 GLU cc_start: 0.8276 (tt0) cc_final: 0.8034 (tt0) REVERT: A 185 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 236 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7675 (mtm180) REVERT: A 243 ASP cc_start: 0.8419 (t0) cc_final: 0.8093 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8513 (tp) cc_final: 0.8237 (tm) REVERT: A 403 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: A 447 ASP cc_start: 0.8532 (m-30) cc_final: 0.8266 (m-30) REVERT: A 530 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8472 (p) REVERT: E 237 TRP cc_start: 0.8648 (t60) cc_final: 0.7947 (t60) REVERT: E 290 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8162 (ttm110) REVERT: E 312 ARG cc_start: 0.8251 (mmp-170) cc_final: 0.7928 (mmp80) REVERT: E 342 ASP cc_start: 0.8677 (t0) cc_final: 0.8302 (t0) REVERT: E 383 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: E 449 GLU cc_start: 0.8668 (tp30) cc_final: 0.8347 (tp30) REVERT: E 600 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8276 (ttt90) REVERT: F 237 TRP cc_start: 0.8318 (t-100) cc_final: 0.7757 (t-100) REVERT: F 271 GLU cc_start: 0.7675 (tp30) cc_final: 0.6978 (tp30) REVERT: F 275 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8448 (ttmm) REVERT: F 312 ARG cc_start: 0.7971 (mmp80) cc_final: 0.7530 (mmp80) REVERT: F 315 ASP cc_start: 0.8761 (m-30) cc_final: 0.8371 (m-30) REVERT: F 324 ASP cc_start: 0.8271 (t0) cc_final: 0.7957 (t70) REVERT: F 329 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8072 (ttm-80) REVERT: F 348 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: F 383 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 418 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 491 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8146 (mtt-85) REVERT: F 507 GLU cc_start: 0.9018 (mt-10) cc_final: 0.7962 (mt-10) REVERT: F 523 GLU cc_start: 0.8038 (tp30) cc_final: 0.7749 (tp30) REVERT: F 525 GLN cc_start: 0.7821 (pm20) cc_final: 0.7489 (pm20) REVERT: F 534 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8408 (mtp85) REVERT: F 575 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 37 SER cc_start: 0.8756 (t) cc_final: 0.8549 (p) REVERT: B 71 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7669 (mmm160) REVERT: B 145 GLU cc_start: 0.8620 (mp0) cc_final: 0.8394 (pm20) REVERT: B 154 ASN cc_start: 0.8605 (t0) cc_final: 0.8320 (t0) REVERT: B 157 ARG cc_start: 0.7338 (ttp80) cc_final: 0.6890 (ttp-170) REVERT: B 184 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 271 GLU cc_start: 0.8348 (tt0) cc_final: 0.7840 (tm-30) REVERT: B 278 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7834 (tm130) REVERT: B 308 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7626 (pm20) REVERT: B 324 ASP cc_start: 0.8530 (t0) cc_final: 0.8313 (t0) REVERT: B 358 SER cc_start: 0.8933 (t) cc_final: 0.8647 (p) REVERT: B 449 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8091 (mm-30) outliers start: 90 outliers final: 44 residues processed: 625 average time/residue: 0.9341 time to fit residues: 649.4350 Evaluate side-chains 601 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 329 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 148 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 0.0060 chunk 218 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 252 GLN C 488 HIS C 513 ASN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 546 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS F 246 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097522 restraints weight = 46063.169| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.23 r_work: 0.3165 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26136 Z= 0.134 Angle : 0.578 8.291 35696 Z= 0.290 Chirality : 0.041 0.162 3961 Planarity : 0.005 0.056 4622 Dihedral : 9.707 90.424 3880 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.53 % Allowed : 19.33 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.62 (0.16), residues: 3184 helix: 1.62 (0.14), residues: 1470 sheet: -0.82 (0.25), residues: 437 loop : -0.49 (0.19), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.008 0.001 TYR C 356 PHE 0.025 0.001 PHE B 59 TRP 0.015 0.001 TRP D 167 HIS 0.008 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26118) covalent geometry : angle 0.57799 / 0.29 (35696) hydrogen bonds : bond 0.03871 / 2.58 ( 1160) hydrogen bonds : angle 4.59460 / 3.34 ( 3252) metal coordination : bond 0.00226 / 0.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 565 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.6854 (OUTLIER) REVERT: C 71 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7381 (ptp90) REVERT: C 77 MET cc_start: 0.8347 (mtp) cc_final: 0.8107 (mtp) REVERT: C 144 LEU cc_start: 0.8386 (pt) cc_final: 0.7988 (mp) REVERT: C 408 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7896 (mtt90) REVERT: C 601 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 71 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7914 (mtm-85) REVERT: D 157 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7773 (ttm110) REVERT: D 203 GLU cc_start: 0.8380 (tp30) cc_final: 0.7729 (tp30) REVERT: D 221 GLU cc_start: 0.8514 (pp20) cc_final: 0.8084 (tm-30) REVERT: D 383 GLU cc_start: 0.8230 (tp30) cc_final: 0.7993 (mm-30) REVERT: D 443 MET cc_start: 0.7670 (mmm) cc_final: 0.7412 (mmm) REVERT: D 575 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: A 25 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 130 GLU cc_start: 0.7764 (tt0) cc_final: 0.7473 (pt0) REVERT: A 140 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: A 181 GLU cc_start: 0.8300 (tt0) cc_final: 0.8077 (tt0) REVERT: A 185 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 236 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7633 (mtm180) REVERT: A 243 ASP cc_start: 0.8399 (t0) cc_final: 0.8074 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8477 (tp) cc_final: 0.8180 (tm) REVERT: A 477 LYS cc_start: 0.8896 (tppt) cc_final: 0.8516 (mppt) REVERT: A 530 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8392 (p) REVERT: E 235 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7401 (mm) REVERT: E 312 ARG cc_start: 0.8257 (mmp-170) cc_final: 0.7963 (mmp80) REVERT: E 342 ASP cc_start: 0.8668 (t0) cc_final: 0.8285 (t0) REVERT: E 449 GLU cc_start: 0.8683 (tp30) cc_final: 0.8324 (tp30) REVERT: E 600 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8271 (ttt90) REVERT: F 237 TRP cc_start: 0.8316 (t-100) cc_final: 0.7736 (t-100) REVERT: F 271 GLU cc_start: 0.7654 (tp30) cc_final: 0.6954 (tp30) REVERT: F 275 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8405 (ttmm) REVERT: F 279 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8005 (mm-30) REVERT: F 312 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7502 (mmp80) REVERT: F 315 ASP cc_start: 0.8773 (m-30) cc_final: 0.8336 (m-30) REVERT: F 324 ASP cc_start: 0.8229 (t0) cc_final: 0.7941 (t70) REVERT: F 348 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: F 383 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 418 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8064 (mt-10) REVERT: F 491 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8090 (mtt-85) REVERT: F 507 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8169 (mt-10) REVERT: F 523 GLU cc_start: 0.8082 (tp30) cc_final: 0.7875 (tp30) REVERT: F 525 GLN cc_start: 0.7831 (pm20) cc_final: 0.7400 (pp30) REVERT: F 534 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8429 (mtp85) REVERT: B 37 SER cc_start: 0.8741 (t) cc_final: 0.8526 (p) REVERT: B 145 GLU cc_start: 0.8594 (mp0) cc_final: 0.8364 (pm20) REVERT: B 154 ASN cc_start: 0.8592 (t0) cc_final: 0.8325 (t0) REVERT: B 184 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 271 GLU cc_start: 0.8334 (tt0) cc_final: 0.7810 (tm-30) REVERT: B 278 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7768 (tm130) REVERT: B 308 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7608 (pm20) REVERT: B 315 ASP cc_start: 0.8705 (m-30) cc_final: 0.8400 (m-30) REVERT: B 324 ASP cc_start: 0.8552 (t0) cc_final: 0.8326 (t0) REVERT: B 358 SER cc_start: 0.8924 (t) cc_final: 0.8625 (p) REVERT: B 449 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7950 (mm-30) outliers start: 92 outliers final: 47 residues processed: 624 average time/residue: 0.8883 time to fit residues: 618.5899 Evaluate side-chains 598 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 543 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 47 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 143 optimal weight: 0.0670 chunk 260 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 282 ASN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 473 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 GLN F 234 HIS F 422 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096747 restraints weight = 45970.770| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.23 r_work: 0.3152 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26136 Z= 0.179 Angle : 0.596 8.544 35696 Z= 0.299 Chirality : 0.042 0.161 3961 Planarity : 0.005 0.047 4622 Dihedral : 9.566 89.907 3876 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.87 % Allowed : 19.98 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.63 (0.16), residues: 3184 helix: 1.64 (0.14), residues: 1458 sheet: -0.83 (0.25), residues: 447 loop : -0.45 (0.19), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 49 TYR 0.008 0.001 TYR E 356 PHE 0.020 0.001 PHE B 51 TRP 0.015 0.001 TRP D 167 HIS 0.008 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (26118) covalent geometry : angle 0.59635 / 0.30 (35696) hydrogen bonds : bond 0.03976 / 2.66 ( 1160) hydrogen bonds : angle 4.58702 / 3.34 ( 3252) metal coordination : bond 0.00314 / 0.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 551 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: C 69 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.6635 (p0) REVERT: C 71 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7471 (ptp90) REVERT: C 77 MET cc_start: 0.8387 (mtp) cc_final: 0.8153 (mtp) REVERT: C 269 HIS cc_start: 0.7872 (m-70) cc_final: 0.7636 (m-70) REVERT: C 408 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7844 (mtt90) REVERT: C 601 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 71 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7919 (mtm-85) REVERT: D 139 ARG cc_start: 0.7249 (ttp80) cc_final: 0.6786 (ppt170) REVERT: D 157 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7786 (ttm110) REVERT: D 203 GLU cc_start: 0.8373 (tp30) cc_final: 0.7752 (tp30) REVERT: D 221 GLU cc_start: 0.8516 (pp20) cc_final: 0.8078 (tm-30) REVERT: D 383 GLU cc_start: 0.8229 (tp30) cc_final: 0.7981 (mm-30) REVERT: D 443 MET cc_start: 0.7636 (mmm) cc_final: 0.7388 (mmm) REVERT: D 526 GLU cc_start: 0.8523 (mp0) cc_final: 0.8263 (mp0) REVERT: A 25 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8113 (mm-40) REVERT: A 29 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 58 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7892 (mtm110) REVERT: A 130 GLU cc_start: 0.7837 (tt0) cc_final: 0.7499 (pt0) REVERT: A 140 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: A 181 GLU cc_start: 0.8275 (tt0) cc_final: 0.8054 (tt0) REVERT: A 185 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 243 ASP cc_start: 0.8405 (t0) cc_final: 0.8086 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8488 (tp) cc_final: 0.8193 (tm) REVERT: A 403 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: A 477 LYS cc_start: 0.8906 (tppt) cc_final: 0.8558 (mppt) REVERT: A 530 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8423 (p) REVERT: E 235 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7420 (mm) REVERT: E 342 ASP cc_start: 0.8690 (t0) cc_final: 0.8290 (t0) REVERT: E 449 GLU cc_start: 0.8692 (tp30) cc_final: 0.8374 (tp30) REVERT: E 600 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8307 (ttt90) REVERT: F 237 TRP cc_start: 0.8322 (t-100) cc_final: 0.7737 (t-100) REVERT: F 271 GLU cc_start: 0.7638 (tp30) cc_final: 0.6943 (tp30) REVERT: F 275 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8427 (ttmm) REVERT: F 279 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8011 (mm-30) REVERT: F 312 ARG cc_start: 0.7964 (mmp80) cc_final: 0.7497 (mmp80) REVERT: F 315 ASP cc_start: 0.8760 (m-30) cc_final: 0.8314 (m-30) REVERT: F 324 ASP cc_start: 0.8255 (t0) cc_final: 0.7941 (t70) REVERT: F 348 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: F 383 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7442 (tm-30) REVERT: F 418 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8095 (mt-10) REVERT: F 491 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8098 (mtt-85) REVERT: F 497 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8560 (ttp80) REVERT: F 507 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8156 (mt-10) REVERT: F 523 GLU cc_start: 0.8093 (tp30) cc_final: 0.7883 (tp30) REVERT: F 525 GLN cc_start: 0.7830 (pm20) cc_final: 0.7362 (pp30) REVERT: B 37 SER cc_start: 0.8755 (t) cc_final: 0.8544 (p) REVERT: B 154 ASN cc_start: 0.8603 (t0) cc_final: 0.8356 (t0) REVERT: B 184 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 271 GLU cc_start: 0.8337 (tt0) cc_final: 0.7801 (tm-30) REVERT: B 278 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7730 (tm130) REVERT: B 308 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7588 (mp0) REVERT: B 315 ASP cc_start: 0.8692 (m-30) cc_final: 0.8433 (m-30) REVERT: B 324 ASP cc_start: 0.8592 (t0) cc_final: 0.8326 (t0) REVERT: B 358 SER cc_start: 0.8926 (t) cc_final: 0.8634 (p) REVERT: B 437 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7040 (tmt-80) REVERT: B 449 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7946 (mm-30) outliers start: 101 outliers final: 62 residues processed: 610 average time/residue: 0.8940 time to fit residues: 607.6062 Evaluate side-chains 612 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 538 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 497 ARG Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 280 optimal weight: 0.0040 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 228 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 277 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 278 GLN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 473 GLN A 488 HIS E 252 GLN E 269 HIS E 375 GLN E 515 GLN F 234 HIS F 422 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097527 restraints weight = 46244.563| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.24 r_work: 0.3173 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26136 Z= 0.137 Angle : 0.593 9.637 35696 Z= 0.297 Chirality : 0.041 0.154 3961 Planarity : 0.005 0.049 4622 Dihedral : 9.469 90.334 3876 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 3.72 % Allowed : 20.48 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.75 (0.16), residues: 3184 helix: 1.70 (0.14), residues: 1461 sheet: -0.73 (0.25), residues: 433 loop : -0.39 (0.19), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 71 TYR 0.016 0.001 TYR D 50 PHE 0.023 0.001 PHE B 51 TRP 0.015 0.001 TRP D 167 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (26118) covalent geometry : angle 0.59342 / 0.30 (35696) hydrogen bonds : bond 0.03646 / 2.44 ( 1160) hydrogen bonds : angle 4.49423 / 3.28 ( 3252) metal coordination : bond 0.00183 / 0.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 563 time to evaluate : 1.209 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: C 69 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.6568 (p0) REVERT: C 269 HIS cc_start: 0.7877 (m-70) cc_final: 0.7641 (m-70) REVERT: C 408 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7823 (mtt90) REVERT: C 601 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8405 (mp) REVERT: D 71 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: D 139 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6858 (ptt90) REVERT: D 157 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7763 (ttm110) REVERT: D 203 GLU cc_start: 0.8359 (tp30) cc_final: 0.7747 (tp30) REVERT: D 221 GLU cc_start: 0.8502 (pp20) cc_final: 0.8036 (tm-30) REVERT: D 383 GLU cc_start: 0.8230 (tp30) cc_final: 0.7983 (mm-30) REVERT: D 443 MET cc_start: 0.7573 (mmm) cc_final: 0.7332 (mmm) REVERT: D 526 GLU cc_start: 0.8513 (mp0) cc_final: 0.8256 (mp0) REVERT: A 1 MET cc_start: 0.8062 (tpp) cc_final: 0.7389 (pp-130) REVERT: A 25 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8110 (mm-40) REVERT: A 29 GLU cc_start: 0.7975 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 53 MET cc_start: 0.8199 (ptt) cc_final: 0.7865 (ppp) REVERT: A 113 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: A 130 GLU cc_start: 0.7846 (tt0) cc_final: 0.7488 (pt0) REVERT: A 140 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6354 (mt-10) REVERT: A 181 GLU cc_start: 0.8269 (tt0) cc_final: 0.8033 (tt0) REVERT: A 185 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 238 LEU cc_start: 0.8781 (tp) cc_final: 0.8429 (tt) REVERT: A 243 ASP cc_start: 0.8425 (t0) cc_final: 0.8110 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8468 (tp) cc_final: 0.8186 (tm) REVERT: A 385 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8265 (ttp80) REVERT: A 403 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7767 (mtm180) REVERT: A 477 LYS cc_start: 0.8889 (tppt) cc_final: 0.8502 (mppt) REVERT: A 530 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8392 (p) REVERT: E 235 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7452 (mm) REVERT: E 342 ASP cc_start: 0.8694 (t0) cc_final: 0.8292 (t0) REVERT: E 449 GLU cc_start: 0.8696 (tp30) cc_final: 0.8336 (tp30) REVERT: E 534 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8480 (mmm-85) REVERT: E 600 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8339 (ttt90) REVERT: F 237 TRP cc_start: 0.8314 (t-100) cc_final: 0.7750 (t-100) REVERT: F 271 GLU cc_start: 0.7614 (tp30) cc_final: 0.6940 (tp30) REVERT: F 275 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8408 (ttmm) REVERT: F 279 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8015 (mm-30) REVERT: F 312 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7500 (mmp80) REVERT: F 315 ASP cc_start: 0.8768 (m-30) cc_final: 0.8363 (m-30) REVERT: F 324 ASP cc_start: 0.8224 (t0) cc_final: 0.7924 (t70) REVERT: F 348 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: F 383 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 418 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8074 (mt-10) REVERT: F 491 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.8114 (mtt-85) REVERT: F 507 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8120 (mt-10) REVERT: F 523 GLU cc_start: 0.8091 (tp30) cc_final: 0.7880 (tp30) REVERT: F 525 GLN cc_start: 0.7886 (pm20) cc_final: 0.7436 (pp30) REVERT: B 37 SER cc_start: 0.8720 (t) cc_final: 0.8515 (p) REVERT: B 184 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8503 (tp) REVERT: B 271 GLU cc_start: 0.8347 (tt0) cc_final: 0.7812 (tm-30) REVERT: B 278 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7742 (tm130) REVERT: B 308 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7574 (mp0) REVERT: B 315 ASP cc_start: 0.8710 (m-30) cc_final: 0.8453 (m-30) REVERT: B 324 ASP cc_start: 0.8583 (t0) cc_final: 0.8341 (t0) REVERT: B 358 SER cc_start: 0.8916 (t) cc_final: 0.8622 (p) REVERT: B 437 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7124 (tmt-80) REVERT: B 449 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7947 (mm-30) outliers start: 97 outliers final: 64 residues processed: 618 average time/residue: 0.9067 time to fit residues: 625.8571 Evaluate side-chains 617 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 542 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 80 optimal weight: 0.0770 chunk 167 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 29 optimal weight: 0.0050 chunk 98 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 289 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 282 ASN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 372 ASN D 473 GLN A 488 HIS E 252 GLN E 375 GLN E 515 GLN F 234 HIS F 422 ASN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098111 restraints weight = 45970.742| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.23 r_work: 0.3179 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26136 Z= 0.123 Angle : 0.605 11.541 35696 Z= 0.303 Chirality : 0.041 0.195 3961 Planarity : 0.005 0.055 4622 Dihedral : 9.366 90.732 3876 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.45 % Rotamer: Outliers : 3.60 % Allowed : 21.47 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.83 (0.16), residues: 3184 helix: 1.78 (0.14), residues: 1462 sheet: -0.65 (0.26), residues: 417 loop : -0.38 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 71 TYR 0.017 0.001 TYR D 50 PHE 0.025 0.001 PHE B 51 TRP 0.015 0.001 TRP A 86 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (26118) covalent geometry : angle 0.60506 / 0.30 (35696) hydrogen bonds : bond 0.03467 / 2.32 ( 1160) hydrogen bonds : angle 4.43174 / 3.24 ( 3252) metal coordination : bond 0.00141 / 0.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 571 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASP cc_start: 0.7920 (p0) cc_final: 0.7713 (p0) REVERT: C 71 ARG cc_start: 0.7471 (ptp90) cc_final: 0.7255 (ptp90) REVERT: C 258 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7778 (tm-30) REVERT: C 269 HIS cc_start: 0.7884 (m-70) cc_final: 0.7625 (m-70) REVERT: C 408 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7772 (mtt90) REVERT: C 601 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8379 (mp) REVERT: D 71 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7878 (mtm-85) REVERT: D 139 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6795 (ptt180) REVERT: D 203 GLU cc_start: 0.8355 (tp30) cc_final: 0.7712 (tp30) REVERT: D 221 GLU cc_start: 0.8499 (pp20) cc_final: 0.8049 (tm-30) REVERT: D 383 GLU cc_start: 0.8233 (tp30) cc_final: 0.7985 (mm-30) REVERT: D 443 MET cc_start: 0.7559 (mmm) cc_final: 0.7326 (mmm) REVERT: D 469 GLU cc_start: 0.8235 (tp30) cc_final: 0.8010 (mm-30) REVERT: A 25 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 89 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: A 113 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: A 130 GLU cc_start: 0.7914 (tt0) cc_final: 0.7564 (pt0) REVERT: A 140 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6323 (mt-10) REVERT: A 181 GLU cc_start: 0.8241 (tt0) cc_final: 0.8016 (tt0) REVERT: A 185 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 238 LEU cc_start: 0.8756 (tp) cc_final: 0.8415 (tt) REVERT: A 243 ASP cc_start: 0.8433 (t0) cc_final: 0.8142 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8462 (tp) cc_final: 0.8185 (tm) REVERT: A 385 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8265 (ttp80) REVERT: A 403 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7849 (mtm180) REVERT: A 477 LYS cc_start: 0.8857 (tppt) cc_final: 0.8476 (mppt) REVERT: A 530 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8384 (p) REVERT: E 235 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7569 (mm) REVERT: E 279 GLU cc_start: 0.8716 (mm-30) cc_final: 0.7733 (tm-30) REVERT: E 342 ASP cc_start: 0.8699 (t0) cc_final: 0.8293 (t0) REVERT: E 348 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: E 385 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8159 (mtp-110) REVERT: E 449 GLU cc_start: 0.8663 (tp30) cc_final: 0.8267 (tp30) REVERT: E 501 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8164 (mm-30) REVERT: E 600 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: F 237 TRP cc_start: 0.8301 (t-100) cc_final: 0.7735 (t-100) REVERT: F 271 GLU cc_start: 0.7595 (tp30) cc_final: 0.6936 (tp30) REVERT: F 275 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8386 (ttmm) REVERT: F 279 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7993 (mm-30) REVERT: F 312 ARG cc_start: 0.7941 (mmp80) cc_final: 0.7334 (mmm160) REVERT: F 315 ASP cc_start: 0.8763 (m-30) cc_final: 0.7838 (m-30) REVERT: F 324 ASP cc_start: 0.8216 (t0) cc_final: 0.7916 (t70) REVERT: F 348 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: F 383 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7407 (tm-30) REVERT: F 418 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8062 (mt-10) REVERT: F 461 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8266 (m90) REVERT: F 491 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8093 (mtt-85) REVERT: F 507 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8121 (mt-10) REVERT: F 521 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8965 (mm) REVERT: F 523 GLU cc_start: 0.8074 (tp30) cc_final: 0.7850 (tp30) REVERT: F 525 GLN cc_start: 0.7897 (pm20) cc_final: 0.7418 (pp30) REVERT: B 37 SER cc_start: 0.8735 (t) cc_final: 0.8496 (p) REVERT: B 184 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 271 GLU cc_start: 0.8320 (tt0) cc_final: 0.7777 (tm-30) REVERT: B 308 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7565 (mp0) REVERT: B 315 ASP cc_start: 0.8712 (m-30) cc_final: 0.8457 (m-30) REVERT: B 324 ASP cc_start: 0.8592 (t0) cc_final: 0.8344 (t0) REVERT: B 358 SER cc_start: 0.8891 (t) cc_final: 0.8592 (p) REVERT: B 418 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: B 437 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7105 (tmt-80) REVERT: B 449 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 477 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8658 (ttmm) REVERT: B 497 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8075 (ttp80) outliers start: 94 outliers final: 60 residues processed: 624 average time/residue: 0.9237 time to fit residues: 643.1989 Evaluate side-chains 626 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 552 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 141 optimal weight: 1.9990 chunk 271 optimal weight: 0.0170 chunk 91 optimal weight: 0.9990 chunk 138 optimal weight: 0.0060 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 244 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 278 GLN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 473 GLN A 488 HIS E 252 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS F 580 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098721 restraints weight = 45995.501| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.24 r_work: 0.3189 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26136 Z= 0.116 Angle : 0.608 13.290 35696 Z= 0.304 Chirality : 0.041 0.153 3961 Planarity : 0.005 0.061 4622 Dihedral : 9.068 91.256 3869 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 3.45 % Allowed : 22.20 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.86 (0.16), residues: 3184 helix: 1.82 (0.14), residues: 1468 sheet: -0.75 (0.25), residues: 428 loop : -0.35 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 49 TYR 0.020 0.001 TYR D 50 PHE 0.016 0.001 PHE B 51 TRP 0.014 0.001 TRP D 167 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (26118) covalent geometry : angle 0.60784 / 0.30 (35696) hydrogen bonds : bond 0.03282 / 2.20 ( 1160) hydrogen bonds : angle 4.38287 / 3.21 ( 3252) metal coordination : bond 0.00098 / 0.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 568 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7502 (mmt-90) REVERT: C 69 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.6681 (OUTLIER) REVERT: C 71 ARG cc_start: 0.7411 (ptp90) cc_final: 0.6881 (ptp90) REVERT: C 258 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7776 (tm-30) REVERT: C 269 HIS cc_start: 0.7838 (m-70) cc_final: 0.7603 (m-70) REVERT: C 315 ASP cc_start: 0.8404 (m-30) cc_final: 0.8186 (m-30) REVERT: C 408 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7650 (mtt90) REVERT: C 601 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8353 (mp) REVERT: D 71 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7949 (mtm-85) REVERT: D 139 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6862 (ptt90) REVERT: D 203 GLU cc_start: 0.8360 (tp30) cc_final: 0.7711 (tp30) REVERT: D 221 GLU cc_start: 0.8534 (pp20) cc_final: 0.8079 (tm-30) REVERT: D 383 GLU cc_start: 0.8249 (tp30) cc_final: 0.7980 (mm-30) REVERT: D 443 MET cc_start: 0.7559 (mmm) cc_final: 0.7298 (mmm) REVERT: D 469 GLU cc_start: 0.8200 (tp30) cc_final: 0.7985 (mm-30) REVERT: D 526 GLU cc_start: 0.8501 (mp0) cc_final: 0.8212 (mp0) REVERT: A 1 MET cc_start: 0.7973 (tpp) cc_final: 0.7241 (pp-130) REVERT: A 25 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8056 (mm-40) REVERT: A 29 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 89 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: A 113 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: A 130 GLU cc_start: 0.7901 (tt0) cc_final: 0.7541 (pt0) REVERT: A 140 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6086 (mm-30) REVERT: A 181 GLU cc_start: 0.8211 (tt0) cc_final: 0.7952 (tt0) REVERT: A 185 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 238 LEU cc_start: 0.8718 (tp) cc_final: 0.8398 (tt) REVERT: A 243 ASP cc_start: 0.8466 (t0) cc_final: 0.8165 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8438 (tp) cc_final: 0.8155 (tm) REVERT: A 385 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8295 (ttp80) REVERT: A 403 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7815 (mtm180) REVERT: A 477 LYS cc_start: 0.8860 (tppt) cc_final: 0.8463 (mppt) REVERT: A 530 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8388 (p) REVERT: E 235 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7584 (mm) REVERT: E 278 GLN cc_start: 0.8539 (tt0) cc_final: 0.8240 (tt0) REVERT: E 279 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7632 (tm-30) REVERT: E 342 ASP cc_start: 0.8679 (t0) cc_final: 0.8267 (t0) REVERT: E 348 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: E 385 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.8131 (mtp-110) REVERT: E 449 GLU cc_start: 0.8595 (tp30) cc_final: 0.8082 (tp30) REVERT: E 501 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8175 (mm-30) REVERT: E 600 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8206 (ttt90) REVERT: F 237 TRP cc_start: 0.8303 (t-100) cc_final: 0.7757 (t-100) REVERT: F 271 GLU cc_start: 0.7592 (tp30) cc_final: 0.6947 (tp30) REVERT: F 275 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8369 (ttmm) REVERT: F 279 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8061 (mm-30) REVERT: F 312 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7437 (mmm160) REVERT: F 324 ASP cc_start: 0.8192 (t0) cc_final: 0.7884 (t70) REVERT: F 348 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: F 383 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7335 (tm-30) REVERT: F 418 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8037 (mt-10) REVERT: F 461 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8264 (m90) REVERT: F 491 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8100 (mtt-85) REVERT: F 507 GLU cc_start: 0.8948 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 523 GLU cc_start: 0.8021 (tp30) cc_final: 0.7794 (tp30) REVERT: F 525 GLN cc_start: 0.7912 (pm20) cc_final: 0.7436 (pp30) REVERT: B 37 SER cc_start: 0.8744 (t) cc_final: 0.8517 (p) REVERT: B 145 GLU cc_start: 0.8345 (pm20) cc_final: 0.8108 (pm20) REVERT: B 184 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (tp) REVERT: B 236 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7952 (mtm110) REVERT: B 271 GLU cc_start: 0.8299 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 308 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7561 (mp0) REVERT: B 315 ASP cc_start: 0.8652 (m-30) cc_final: 0.8391 (m-30) REVERT: B 324 ASP cc_start: 0.8604 (t0) cc_final: 0.8363 (t0) REVERT: B 358 SER cc_start: 0.8848 (t) cc_final: 0.8546 (p) REVERT: B 449 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 477 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8634 (ttmm) REVERT: B 497 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7972 (ttp80) outliers start: 90 outliers final: 56 residues processed: 622 average time/residue: 0.9089 time to fit residues: 630.7924 Evaluate side-chains 624 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 557 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 580 GLN Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 311 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 241 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 282 ASN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 372 ASN D 473 GLN A 488 HIS E 252 GLN E 269 HIS E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS F 488 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098105 restraints weight = 46149.500| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.23 r_work: 0.3180 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26136 Z= 0.138 Angle : 0.629 15.714 35696 Z= 0.314 Chirality : 0.041 0.151 3961 Planarity : 0.005 0.073 4622 Dihedral : 9.003 90.823 3867 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.18 % Allowed : 23.12 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.86 (0.16), residues: 3184 helix: 1.83 (0.14), residues: 1464 sheet: -0.75 (0.25), residues: 428 loop : -0.36 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 139 TYR 0.021 0.001 TYR D 50 PHE 0.053 0.001 PHE B 51 TRP 0.016 0.001 TRP A 86 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (26118) covalent geometry : angle 0.62899 / 0.31 (35696) hydrogen bonds : bond 0.03409 / 2.29 ( 1160) hydrogen bonds : angle 4.39663 / 3.22 ( 3252) metal coordination : bond 0.00207 / 0.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 562 time to evaluate : 1.000 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: C 2 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7538 (mmt-90) REVERT: C 164 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: C 258 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7808 (tm-30) REVERT: C 269 HIS cc_start: 0.7856 (m-70) cc_final: 0.7617 (m-70) REVERT: C 315 ASP cc_start: 0.8375 (m-30) cc_final: 0.8171 (m-30) REVERT: C 408 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7542 (mtt90) REVERT: C 601 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8357 (mp) REVERT: D 71 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: D 139 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6862 (ptt90) REVERT: D 157 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (ttm110) REVERT: D 203 GLU cc_start: 0.8369 (tp30) cc_final: 0.7709 (tp30) REVERT: D 221 GLU cc_start: 0.8530 (pp20) cc_final: 0.8106 (tm-30) REVERT: D 383 GLU cc_start: 0.8236 (tp30) cc_final: 0.7968 (mm-30) REVERT: D 443 MET cc_start: 0.7586 (mmm) cc_final: 0.7345 (mmm) REVERT: D 526 GLU cc_start: 0.8505 (mp0) cc_final: 0.8214 (mp0) REVERT: A 25 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8050 (mm-40) REVERT: A 89 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: A 113 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: A 130 GLU cc_start: 0.7954 (tt0) cc_final: 0.7603 (pt0) REVERT: A 140 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: A 181 GLU cc_start: 0.8247 (tt0) cc_final: 0.8014 (tt0) REVERT: A 185 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 238 LEU cc_start: 0.8716 (tp) cc_final: 0.8409 (tt) REVERT: A 243 ASP cc_start: 0.8463 (t0) cc_final: 0.8168 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8460 (tp) cc_final: 0.8199 (tm) REVERT: A 385 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8309 (ttp80) REVERT: A 477 LYS cc_start: 0.8854 (tppt) cc_final: 0.8466 (mppt) REVERT: A 530 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8424 (p) REVERT: E 235 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7576 (mm) REVERT: E 279 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7696 (tm-30) REVERT: E 342 ASP cc_start: 0.8681 (t0) cc_final: 0.8269 (t0) REVERT: E 348 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: E 385 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8125 (mtp-110) REVERT: E 449 GLU cc_start: 0.8641 (tp30) cc_final: 0.8138 (tp30) REVERT: E 501 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8194 (mm-30) REVERT: E 600 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8201 (ttt90) REVERT: F 237 TRP cc_start: 0.8300 (t-100) cc_final: 0.7736 (t-100) REVERT: F 271 GLU cc_start: 0.7604 (tp30) cc_final: 0.6956 (tp30) REVERT: F 275 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8380 (ttmm) REVERT: F 279 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8052 (mm-30) REVERT: F 312 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7445 (mmm160) REVERT: F 324 ASP cc_start: 0.8208 (t0) cc_final: 0.7896 (t70) REVERT: F 348 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: F 383 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7348 (tm-30) REVERT: F 418 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7999 (mt-10) REVERT: F 461 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8276 (m90) REVERT: F 491 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8105 (mtt-85) REVERT: F 507 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8064 (mt-10) REVERT: F 523 GLU cc_start: 0.7996 (tp30) cc_final: 0.7779 (tp30) REVERT: F 525 GLN cc_start: 0.7912 (pm20) cc_final: 0.7419 (pp30) REVERT: B 37 SER cc_start: 0.8742 (t) cc_final: 0.8513 (p) REVERT: B 53 MET cc_start: 0.7838 (ppp) cc_final: 0.7379 (tmm) REVERT: B 184 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8316 (tp) REVERT: B 236 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7986 (mtm110) REVERT: B 271 GLU cc_start: 0.8295 (tt0) cc_final: 0.7757 (tm-30) REVERT: B 278 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 308 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7568 (mp0) REVERT: B 315 ASP cc_start: 0.8655 (m-30) cc_final: 0.8379 (m-30) REVERT: B 324 ASP cc_start: 0.8623 (t0) cc_final: 0.8376 (t0) REVERT: B 358 SER cc_start: 0.8883 (t) cc_final: 0.8592 (p) REVERT: B 449 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 477 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8636 (ttmm) outliers start: 83 outliers final: 57 residues processed: 611 average time/residue: 0.9069 time to fit residues: 618.4375 Evaluate side-chains 615 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 546 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 272 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 302 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 169 GLN D 372 ASN A 488 HIS E 252 GLN E 282 ASN E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS F 422 ASN F 488 HIS F 580 GLN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097882 restraints weight = 46118.571| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.23 r_work: 0.3173 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26136 Z= 0.150 Angle : 0.653 17.839 35696 Z= 0.325 Chirality : 0.042 0.167 3961 Planarity : 0.005 0.068 4622 Dihedral : 8.938 90.087 3867 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 2.95 % Allowed : 23.31 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.85 (0.16), residues: 3184 helix: 1.80 (0.14), residues: 1460 sheet: -0.69 (0.25), residues: 436 loop : -0.37 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 49 TYR 0.021 0.001 TYR D 50 PHE 0.014 0.001 PHE B 59 TRP 0.015 0.001 TRP D 167 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26118) covalent geometry : angle 0.65259 / 0.32 (35696) hydrogen bonds : bond 0.03536 / 2.38 ( 1160) hydrogen bonds : angle 4.40064 / 3.22 ( 3252) metal coordination : bond 0.00233 / 0.14 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 563 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7610 (mmt-90) REVERT: C 164 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: C 258 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7791 (tm-30) REVERT: C 269 HIS cc_start: 0.7879 (m-70) cc_final: 0.7632 (m-70) REVERT: C 315 ASP cc_start: 0.8365 (m-30) cc_final: 0.8104 (m-30) REVERT: C 408 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7561 (mtt90) REVERT: C 601 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8368 (mp) REVERT: D 71 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7995 (mtm-85) REVERT: D 139 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6769 (ppt170) REVERT: D 157 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7820 (ttm110) REVERT: D 185 GLN cc_start: 0.6888 (mp10) cc_final: 0.6680 (pm20) REVERT: D 203 GLU cc_start: 0.8377 (tp30) cc_final: 0.7704 (tp30) REVERT: D 221 GLU cc_start: 0.8531 (pp20) cc_final: 0.8098 (tm-30) REVERT: D 383 GLU cc_start: 0.8245 (tp30) cc_final: 0.7872 (tp30) REVERT: D 526 GLU cc_start: 0.8506 (mp0) cc_final: 0.8211 (mp0) REVERT: A 25 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8052 (mm-40) REVERT: A 89 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: A 113 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 130 GLU cc_start: 0.7972 (tt0) cc_final: 0.7616 (pt0) REVERT: A 140 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6415 (mt-10) REVERT: A 181 GLU cc_start: 0.8281 (tt0) cc_final: 0.8038 (tt0) REVERT: A 185 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 238 LEU cc_start: 0.8726 (tp) cc_final: 0.8423 (tt) REVERT: A 243 ASP cc_start: 0.8467 (t0) cc_final: 0.8191 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8473 (tp) cc_final: 0.8201 (tm) REVERT: A 385 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8326 (ttp80) REVERT: A 477 LYS cc_start: 0.8865 (tppt) cc_final: 0.8480 (mppt) REVERT: A 530 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8430 (p) REVERT: E 235 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7574 (mm) REVERT: E 278 GLN cc_start: 0.8564 (tt0) cc_final: 0.8262 (tt0) REVERT: E 279 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7672 (tm-30) REVERT: E 312 ARG cc_start: 0.8156 (mmp-170) cc_final: 0.7760 (mmp-170) REVERT: E 342 ASP cc_start: 0.8695 (t0) cc_final: 0.8281 (t0) REVERT: E 348 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: E 385 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8131 (mtp-110) REVERT: E 449 GLU cc_start: 0.8657 (tp30) cc_final: 0.8148 (tp30) REVERT: E 453 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8674 (mmt90) REVERT: E 600 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8157 (ttt90) REVERT: F 237 TRP cc_start: 0.8306 (t-100) cc_final: 0.7746 (t-100) REVERT: F 271 GLU cc_start: 0.7624 (tp30) cc_final: 0.6976 (tp30) REVERT: F 275 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8382 (ttmm) REVERT: F 279 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8066 (mm-30) REVERT: F 324 ASP cc_start: 0.8224 (t0) cc_final: 0.7918 (t70) REVERT: F 348 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: F 383 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7365 (tm-30) REVERT: F 418 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7996 (mt-10) REVERT: F 461 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8309 (m90) REVERT: F 491 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8106 (mtt-85) REVERT: F 507 GLU cc_start: 0.8983 (mt-10) cc_final: 0.7953 (mt-10) REVERT: F 523 GLU cc_start: 0.8002 (tp30) cc_final: 0.7760 (tp30) REVERT: F 525 GLN cc_start: 0.7908 (pm20) cc_final: 0.7392 (pp30) REVERT: B 37 SER cc_start: 0.8730 (t) cc_final: 0.8516 (p) REVERT: B 53 MET cc_start: 0.7812 (ppp) cc_final: 0.7336 (tmm) REVERT: B 106 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7714 (mmtp) REVERT: B 157 ARG cc_start: 0.7354 (ttp80) cc_final: 0.7020 (ttp80) REVERT: B 184 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (tm) REVERT: B 271 GLU cc_start: 0.8310 (tt0) cc_final: 0.7769 (tm-30) REVERT: B 278 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 308 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7578 (pm20) REVERT: B 315 ASP cc_start: 0.8640 (m-30) cc_final: 0.8390 (m-30) REVERT: B 324 ASP cc_start: 0.8648 (t0) cc_final: 0.8400 (t0) REVERT: B 358 SER cc_start: 0.8895 (t) cc_final: 0.8607 (p) REVERT: B 437 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7122 (tmt-80) REVERT: B 449 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 477 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8629 (ttmm) REVERT: B 534 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8631 (mmt90) outliers start: 77 outliers final: 58 residues processed: 608 average time/residue: 0.8930 time to fit residues: 605.8143 Evaluate side-chains 630 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 559 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 22 optimal weight: 0.6980 chunk 104 optimal weight: 0.0570 chunk 194 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 151 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 282 ASN C 488 HIS C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 169 GLN A 89 GLN A 488 HIS E 252 GLN E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 591 GLN F 234 HIS F 488 HIS F 580 GLN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098682 restraints weight = 45956.536| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.23 r_work: 0.3187 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26136 Z= 0.129 Angle : 0.647 18.352 35696 Z= 0.324 Chirality : 0.041 0.162 3961 Planarity : 0.005 0.062 4622 Dihedral : 8.856 90.000 3867 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.88 % Allowed : 23.70 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.86 (0.16), residues: 3184 helix: 1.81 (0.14), residues: 1465 sheet: -0.69 (0.26), residues: 428 loop : -0.36 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 139 TYR 0.023 0.001 TYR D 50 PHE 0.025 0.001 PHE A 51 TRP 0.017 0.001 TRP A 86 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (26118) covalent geometry : angle 0.64709 / 0.32 (35696) hydrogen bonds : bond 0.03415 / 2.31 ( 1160) hydrogen bonds : angle 4.39461 / 3.22 ( 3252) metal coordination : bond 0.00134 / 0.08 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11979.55 seconds wall clock time: 204 minutes 6.34 seconds (12246.34 seconds total)