Starting phenix.real_space_refine on Sun Jul 5 06:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1h_65540/07_2026/9w1h_65540_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1h_65540/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9w1h_65540/07_2026/9w1h_65540_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1h_65540/07_2026/9w1h_65540_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1h_65540/07_2026/9w1h_65540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1h_65540/07_2026/9w1h_65540.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 6.21, per 1000 atoms: 0.24 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: 0.83 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: 5.07 Time building geometry restraints manager: 3.08 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: 35368 2.66 - 5.32: 302 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=" 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 angle pdb=" N SER D 220 " pdb=" CA SER D 220 " pdb=" C SER D 220 " ideal model delta sigma weight residual 113.17 108.11 5.06 1.26e+00 6.30e-01 1.61e+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: 3655 0.081 - 0.161: 284 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: 4.080 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.320 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- 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 : 0.583 13.301 35696 Z= 0.323 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 0.58343 / 0.32 (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 : 1.050 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: 0.8772 time to fit residues: 643.3661 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 : 0.984 ------------------------------------------------------------------------------- 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 169 GLN 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097282 restraints weight = 45639.313| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.24 r_work: 0.3161 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 26136 Z= 0.154 Angle : 0.618 12.364 35696 Z= 0.312 Chirality : 0.042 0.148 3961 Planarity : 0.005 0.052 4622 Dihedral : 10.371 91.349 3915 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 3.60 % Allowed : 16.95 % Favored : 79.45 % 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: -0.98 (0.25), residues: 444 loop : -0.55 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 333 TYR 0.008 0.001 TYR B 98 PHE 0.014 0.001 PHE C 59 TRP 0.013 0.001 TRP C 364 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (26118) covalent geometry : angle 0.61776 / 0.31 (35696) hydrogen bonds : bond 0.04697 / 3.12 ( 1160) hydrogen bonds : angle 5.03588 / 3.66 ( 3252) metal coordination : bond 0.04629 / 2.32 ( 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 678 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 584 time to evaluate : 1.021 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: 0.7833 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: C 157 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7820 (mtm180) REVERT: C 279 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8501 (mm-30) REVERT: C 408 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7823 (mtt90) REVERT: C 601 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8412 (mp) REVERT: D 71 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: D 157 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7931 (ttm110) REVERT: D 203 GLU cc_start: 0.8413 (tp30) cc_final: 0.7804 (tp30) REVERT: D 221 GLU cc_start: 0.8441 (pp20) cc_final: 0.8008 (tm-30) REVERT: D 383 GLU cc_start: 0.8256 (tp30) cc_final: 0.8020 (mm-30) REVERT: D 443 MET cc_start: 0.7581 (mmm) cc_final: 0.7335 (mmm) REVERT: D 575 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 25 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8077 (mm-40) REVERT: A 74 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 130 GLU cc_start: 0.7905 (tt0) cc_final: 0.7620 (tt0) REVERT: A 140 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5776 (mt-10) REVERT: A 142 SER cc_start: 0.8597 (t) cc_final: 0.8387 (m) REVERT: A 157 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.8520 (mtm-85) REVERT: A 181 GLU cc_start: 0.8292 (tt0) cc_final: 0.8046 (tt0) REVERT: A 185 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 221 GLU cc_start: 0.8146 (pp20) cc_final: 0.7897 (pp20) REVERT: A 236 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7620 (mtm180) REVERT: A 243 ASP cc_start: 0.8407 (t0) cc_final: 0.8064 (t0) REVERT: A 307 LEU cc_start: 0.8521 (tp) cc_final: 0.8234 (tm) REVERT: A 530 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8529 (p) REVERT: E 237 TRP cc_start: 0.8642 (t60) cc_final: 0.7973 (t60) REVERT: E 248 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8086 (ttmm) REVERT: E 290 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8164 (ttm110) REVERT: E 312 ARG cc_start: 0.8219 (mmp-170) cc_final: 0.8016 (mmp80) REVERT: E 324 ASP cc_start: 0.8145 (t0) cc_final: 0.7848 (t0) REVERT: E 342 ASP cc_start: 0.8668 (t0) cc_final: 0.8381 (t0) REVERT: E 449 GLU cc_start: 0.8639 (tp30) cc_final: 0.8115 (tp30) REVERT: E 600 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8275 (ttt90) REVERT: F 237 TRP cc_start: 0.8306 (t-100) cc_final: 0.7736 (t-100) REVERT: F 271 GLU cc_start: 0.7628 (tp30) cc_final: 0.6964 (tp30) REVERT: F 275 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8416 (ttmm) REVERT: F 312 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7552 (mmp80) REVERT: F 315 ASP cc_start: 0.8776 (m-30) cc_final: 0.8409 (m-30) REVERT: F 324 ASP cc_start: 0.8193 (t0) cc_final: 0.7838 (t70) REVERT: F 329 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8067 (ttm-80) REVERT: F 348 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: F 383 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7448 (tm-30) REVERT: F 418 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7936 (mt-10) REVERT: F 491 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8077 (mtt-85) REVERT: F 507 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8430 (mt-10) REVERT: F 523 GLU cc_start: 0.7920 (tp30) cc_final: 0.7669 (tp30) REVERT: F 525 GLN cc_start: 0.7798 (pm20) cc_final: 0.7524 (pm20) REVERT: F 534 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8417 (mtp85) REVERT: B 71 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7658 (mmm160) REVERT: B 145 GLU cc_start: 0.8627 (mp0) cc_final: 0.8390 (pm20) REVERT: B 154 ASN cc_start: 0.8569 (t0) cc_final: 0.8270 (t0) REVERT: B 184 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 271 GLU cc_start: 0.8316 (tt0) cc_final: 0.7812 (tm-30) REVERT: B 278 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 308 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7614 (pm20) REVERT: B 358 SER cc_start: 0.8949 (t) cc_final: 0.8662 (p) REVERT: B 430 ASP cc_start: 0.8363 (t0) cc_final: 0.8152 (t0) outliers start: 94 outliers final: 47 residues processed: 629 average time/residue: 0.9066 time to fit residues: 634.5708 Evaluate side-chains 611 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 553 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain C residue 128 LEU 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 321 LEU 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 530 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 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: 0.4980 chunk 217 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 chunk 90 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 473 GLN D 546 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS A 488 HIS E 375 GLN E 376 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097485 restraints weight = 46246.995| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.24 r_work: 0.3166 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26136 Z= 0.135 Angle : 0.576 9.518 35696 Z= 0.290 Chirality : 0.041 0.144 3961 Planarity : 0.005 0.045 4622 Dihedral : 9.881 92.341 3883 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.41 % Allowed : 18.33 % Favored : 78.26 % 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: 0.53 (0.16), residues: 3184 helix: 1.55 (0.14), residues: 1471 sheet: -0.87 (0.25), residues: 432 loop : -0.55 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.011 0.001 TYR A 50 PHE 0.020 0.001 PHE A 59 TRP 0.014 0.001 TRP D 167 HIS 0.007 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (26118) covalent geometry : angle 0.57617 / 0.29 (35696) hydrogen bonds : bond 0.04126 / 2.74 ( 1160) hydrogen bonds : angle 4.73513 / 3.44 ( 3252) metal coordination : bond 0.00267 / 0.15 ( 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 665 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 576 time to evaluate : 0.860 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: 0.8181 (p0) cc_final: 0.7852 (p0) REVERT: C 71 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7377 (ptp90) REVERT: C 132 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8174 (ptp90) REVERT: C 207 GLU cc_start: 0.8703 (tp30) cc_final: 0.8335 (mp0) REVERT: C 269 HIS cc_start: 0.7848 (m-70) cc_final: 0.7631 (m-70) REVERT: C 408 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7825 (mtt90) REVERT: C 601 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8408 (mp) REVERT: D 71 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7823 (mtm-85) REVERT: D 157 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7801 (ttm110) REVERT: D 203 GLU cc_start: 0.8389 (tp30) cc_final: 0.7709 (tp30) REVERT: D 221 GLU cc_start: 0.8489 (pp20) cc_final: 0.8059 (tm-30) REVERT: D 383 GLU cc_start: 0.8239 (tp30) cc_final: 0.7954 (mm-30) REVERT: D 397 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7611 (mtt180) REVERT: D 443 MET cc_start: 0.7688 (mmm) cc_final: 0.7383 (mmm) REVERT: A 25 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8089 (mm-40) REVERT: A 29 GLU cc_start: 0.8172 (tt0) cc_final: 0.7658 (mm-30) REVERT: A 53 MET cc_start: 0.8275 (ptt) cc_final: 0.7967 (ppp) REVERT: A 58 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7773 (mtm110) REVERT: A 74 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 140 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: A 142 SER cc_start: 0.8546 (t) cc_final: 0.8262 (p) REVERT: A 157 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8464 (mtm-85) REVERT: A 181 GLU cc_start: 0.8266 (tt0) cc_final: 0.8065 (tt0) REVERT: A 185 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 221 GLU cc_start: 0.8167 (pp20) cc_final: 0.7865 (pp20) REVERT: A 236 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7635 (mtm180) REVERT: A 243 ASP cc_start: 0.8419 (t0) cc_final: 0.8080 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8492 (tp) cc_final: 0.8199 (tm) REVERT: A 385 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8080 (ttp80) REVERT: A 477 LYS cc_start: 0.8908 (tppt) cc_final: 0.8521 (mppt) REVERT: A 530 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (p) REVERT: E 237 TRP cc_start: 0.8626 (t60) cc_final: 0.7939 (t60) REVERT: E 290 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8145 (ttm110) REVERT: E 312 ARG cc_start: 0.8238 (mmp-170) cc_final: 0.7918 (mmp80) REVERT: E 342 ASP cc_start: 0.8681 (t0) cc_final: 0.8294 (t0) REVERT: E 383 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: E 449 GLU cc_start: 0.8674 (tp30) cc_final: 0.8311 (tp30) REVERT: E 600 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8215 (ttt90) REVERT: F 237 TRP cc_start: 0.8318 (t-100) cc_final: 0.7757 (t-100) REVERT: F 271 GLU cc_start: 0.7659 (tp30) cc_final: 0.6968 (tp30) REVERT: F 275 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8432 (ttmm) REVERT: F 312 ARG cc_start: 0.7972 (mmp80) cc_final: 0.7544 (mmp80) REVERT: F 315 ASP cc_start: 0.8770 (m-30) cc_final: 0.8364 (m-30) REVERT: F 324 ASP cc_start: 0.8237 (t0) cc_final: 0.7929 (t70) REVERT: F 329 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8061 (ttm-80) REVERT: F 348 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: F 383 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7474 (tm-30) REVERT: F 418 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7911 (mt-10) REVERT: F 491 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8143 (mtt-85) REVERT: F 507 GLU cc_start: 0.9024 (mt-10) cc_final: 0.7989 (mt-10) REVERT: F 523 GLU cc_start: 0.8068 (tp30) cc_final: 0.7789 (tp30) REVERT: F 525 GLN cc_start: 0.7846 (pm20) cc_final: 0.7510 (pm20) REVERT: F 534 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8447 (mtp85) REVERT: B 37 SER cc_start: 0.8733 (t) cc_final: 0.8522 (p) REVERT: B 71 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7627 (mmm160) REVERT: B 145 GLU cc_start: 0.8639 (mp0) cc_final: 0.8412 (pm20) REVERT: B 154 ASN cc_start: 0.8597 (t0) cc_final: 0.8318 (t0) REVERT: B 184 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 271 GLU cc_start: 0.8327 (tt0) cc_final: 0.7807 (tm-30) REVERT: B 278 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7877 (tm130) REVERT: B 308 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7612 (pm20) REVERT: B 324 ASP cc_start: 0.8491 (t0) cc_final: 0.8260 (t0) REVERT: B 358 SER cc_start: 0.8923 (t) cc_final: 0.8635 (p) outliers start: 89 outliers final: 42 residues processed: 630 average time/residue: 0.8850 time to fit residues: 621.1482 Evaluate side-chains 599 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 548 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 290 ARG 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 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 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 530 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 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 302 GLU 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: 2.9990 chunk 258 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 278 GLN C 488 HIS C 513 ASN C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 169 GLN D 473 GLN D 546 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS E 269 HIS E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097189 restraints weight = 46102.846| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.23 r_work: 0.3163 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26136 Z= 0.153 Angle : 0.585 8.765 35696 Z= 0.293 Chirality : 0.042 0.160 3961 Planarity : 0.005 0.056 4622 Dihedral : 9.654 92.728 3876 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 3.37 % Allowed : 19.21 % Favored : 77.42 % 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: 0.61 (0.16), residues: 3184 helix: 1.62 (0.14), residues: 1471 sheet: -0.89 (0.25), residues: 443 loop : -0.47 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 49 TYR 0.008 0.001 TYR C 356 PHE 0.022 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 0.00361 / 0.15 (26118) covalent geometry : angle 0.58546 / 0.29 (35696) hydrogen bonds : bond 0.03912 / 2.61 ( 1160) hydrogen bonds : angle 4.60384 / 3.35 ( 3252) metal coordination : bond 0.00261 / 0.15 ( 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 655 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 567 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.6744 (OUTLIER) REVERT: C 71 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7344 (ptp90) REVERT: C 144 LEU cc_start: 0.8395 (pt) cc_final: 0.7983 (mt) REVERT: C 203 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 207 GLU cc_start: 0.8696 (tp30) cc_final: 0.8313 (mp0) REVERT: C 269 HIS cc_start: 0.7833 (m-70) cc_final: 0.7618 (m-70) REVERT: C 408 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7834 (mtt90) REVERT: C 601 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8372 (mp) REVERT: D 71 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: D 157 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7811 (ttm110) REVERT: D 203 GLU cc_start: 0.8353 (tp30) cc_final: 0.7725 (tp30) REVERT: D 221 GLU cc_start: 0.8483 (pp20) cc_final: 0.8054 (tm-30) REVERT: D 383 GLU cc_start: 0.8210 (tp30) cc_final: 0.7969 (mm-30) REVERT: D 443 MET cc_start: 0.7664 (mmm) cc_final: 0.7358 (mmm) REVERT: D 575 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: A 25 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8102 (mm-40) REVERT: A 29 GLU cc_start: 0.8146 (tt0) cc_final: 0.7518 (mm-30) REVERT: A 58 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7748 (mpp80) REVERT: A 140 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: A 142 SER cc_start: 0.8594 (t) cc_final: 0.8275 (p) REVERT: A 149 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: A 181 GLU cc_start: 0.8273 (tt0) cc_final: 0.8050 (tt0) REVERT: A 185 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 236 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7631 (mtm180) REVERT: A 243 ASP cc_start: 0.8409 (t0) cc_final: 0.8080 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8491 (tp) cc_final: 0.8208 (tm) REVERT: A 385 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8035 (ttp80) REVERT: A 477 LYS cc_start: 0.8906 (tppt) cc_final: 0.8528 (mppt) REVERT: A 530 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8441 (p) REVERT: E 290 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8175 (ttm110) REVERT: E 342 ASP cc_start: 0.8677 (t0) cc_final: 0.8289 (t0) REVERT: E 385 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8175 (mtp-110) REVERT: E 449 GLU cc_start: 0.8695 (tp30) cc_final: 0.8338 (tp30) REVERT: E 600 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8278 (ttt90) REVERT: F 237 TRP cc_start: 0.8326 (t-100) cc_final: 0.7739 (t-100) REVERT: F 271 GLU cc_start: 0.7655 (tp30) cc_final: 0.6953 (tp30) REVERT: F 275 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8414 (ttmm) REVERT: F 279 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8038 (mm-30) REVERT: F 312 ARG cc_start: 0.7959 (mmp80) cc_final: 0.7532 (mmp80) REVERT: F 315 ASP cc_start: 0.8765 (m-30) cc_final: 0.8368 (m-30) REVERT: F 324 ASP cc_start: 0.8221 (t0) cc_final: 0.7930 (t70) REVERT: F 329 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8084 (ttm-80) REVERT: F 348 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: F 383 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7417 (tm-30) REVERT: F 418 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8093 (mt-10) REVERT: F 491 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8122 (mtt-85) REVERT: F 507 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8194 (mt-10) REVERT: F 523 GLU cc_start: 0.8086 (tp30) cc_final: 0.7879 (tp30) REVERT: F 525 GLN cc_start: 0.7860 (pm20) cc_final: 0.7406 (pp30) REVERT: F 534 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8475 (mtp85) REVERT: B 37 SER cc_start: 0.8741 (t) cc_final: 0.8526 (p) REVERT: B 77 MET cc_start: 0.8525 (tmt) cc_final: 0.8260 (tmt) REVERT: B 145 GLU cc_start: 0.8581 (mp0) cc_final: 0.8381 (pm20) REVERT: B 154 ASN cc_start: 0.8594 (t0) cc_final: 0.8337 (t0) REVERT: B 184 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 271 GLU cc_start: 0.8358 (tt0) cc_final: 0.7830 (tm-30) REVERT: B 278 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7752 (tm130) REVERT: B 302 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: B 308 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7585 (mp0) REVERT: B 324 ASP cc_start: 0.8535 (t0) cc_final: 0.8310 (t0) REVERT: B 358 SER cc_start: 0.8931 (t) cc_final: 0.8632 (p) REVERT: B 435 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6940 (mm-30) outliers start: 88 outliers final: 50 residues processed: 617 average time/residue: 0.9131 time to fit residues: 627.5825 Evaluate side-chains 613 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 552 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain C residue 248 LYS 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 122 CYS 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 311 MET Chi-restraints excluded: chain D residue 313 LEU 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 96 HIS 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 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 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 243 ASP 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 460 VAL Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR 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 122 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 GLU 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: 2.9990 chunk 313 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 267 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 0.0170 chunk 260 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 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 ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS F 422 ASN F 488 HIS ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097650 restraints weight = 45918.189| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.22 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26136 Z= 0.132 Angle : 0.583 8.768 35696 Z= 0.291 Chirality : 0.041 0.146 3961 Planarity : 0.005 0.047 4622 Dihedral : 9.528 93.287 3875 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 19.17 % Favored : 76.84 % 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: 0.71 (0.16), residues: 3184 helix: 1.71 (0.14), residues: 1463 sheet: -0.85 (0.25), residues: 424 loop : -0.43 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 71 TYR 0.008 0.001 TYR C 356 PHE 0.019 0.001 PHE B 51 TRP 0.014 0.001 TRP D 167 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26118) covalent geometry : angle 0.58271 / 0.29 (35696) hydrogen bonds : bond 0.03669 / 2.44 ( 1160) hydrogen bonds : angle 4.50021 / 3.28 ( 3252) metal coordination : bond 0.00196 / 0.12 ( 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 682 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 578 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.6515 (p0) REVERT: C 77 MET cc_start: 0.8403 (mtp) cc_final: 0.8186 (mtp) REVERT: C 132 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8210 (ptp90) REVERT: C 258 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7791 (tm-30) REVERT: C 269 HIS cc_start: 0.7858 (m-70) cc_final: 0.7611 (m-70) REVERT: C 408 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7813 (mtt90) REVERT: C 601 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8391 (mp) REVERT: D 71 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7923 (mtm-85) REVERT: D 139 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6892 (ppt170) REVERT: D 157 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7770 (ttm110) REVERT: D 203 GLU cc_start: 0.8330 (tp30) cc_final: 0.7753 (tp30) REVERT: D 221 GLU cc_start: 0.8518 (pp20) cc_final: 0.8035 (tm-30) REVERT: D 383 GLU cc_start: 0.8222 (tp30) cc_final: 0.7965 (mm-30) REVERT: D 443 MET cc_start: 0.7640 (mmm) cc_final: 0.7355 (mmm) REVERT: D 526 GLU cc_start: 0.8502 (mp0) cc_final: 0.8236 (mp0) REVERT: A 25 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8084 (mm-40) REVERT: A 29 GLU cc_start: 0.8154 (tt0) cc_final: 0.7538 (mm-30) REVERT: A 58 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7737 (mpp80) REVERT: A 59 PHE cc_start: 0.7950 (m-10) cc_final: 0.7655 (m-10) REVERT: A 139 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7261 (ptm160) REVERT: A 140 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6219 (mt-10) REVERT: A 142 SER cc_start: 0.8575 (t) cc_final: 0.8213 (p) REVERT: A 181 GLU cc_start: 0.8265 (tt0) cc_final: 0.8044 (tt0) REVERT: A 185 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 243 ASP cc_start: 0.8408 (t0) cc_final: 0.8076 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8451 (tp) cc_final: 0.8171 (tm) REVERT: A 385 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8169 (ttp80) REVERT: A 477 LYS cc_start: 0.8897 (tppt) cc_final: 0.8503 (mppt) REVERT: A 530 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8402 (p) REVERT: E 342 ASP cc_start: 0.8698 (t0) cc_final: 0.8283 (t0) REVERT: E 449 GLU cc_start: 0.8684 (tp30) cc_final: 0.8329 (tp30) REVERT: E 600 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8246 (ttt90) REVERT: F 237 TRP cc_start: 0.8304 (t-100) cc_final: 0.7756 (t-100) REVERT: F 271 GLU cc_start: 0.7617 (tp30) cc_final: 0.6935 (tp30) REVERT: F 275 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8431 (ttmm) REVERT: F 312 ARG cc_start: 0.7949 (mmp80) cc_final: 0.7526 (mmp80) REVERT: F 315 ASP cc_start: 0.8767 (m-30) cc_final: 0.8385 (m-30) REVERT: F 324 ASP cc_start: 0.8206 (t0) cc_final: 0.7894 (t70) REVERT: F 348 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: F 383 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7449 (tm-30) REVERT: F 418 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8004 (mt-10) REVERT: F 491 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8120 (mtt-85) REVERT: F 507 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8543 (mp0) REVERT: F 523 GLU cc_start: 0.8085 (tp30) cc_final: 0.7881 (tp30) REVERT: F 525 GLN cc_start: 0.7864 (pm20) cc_final: 0.7403 (pp30) REVERT: F 534 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8489 (mtp85) REVERT: B 37 SER cc_start: 0.8751 (t) cc_final: 0.8524 (p) REVERT: B 69 ASP cc_start: 0.7416 (m-30) cc_final: 0.7165 (m-30) REVERT: B 154 ASN cc_start: 0.8591 (t0) cc_final: 0.8321 (t0) REVERT: B 184 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 247 ASP cc_start: 0.8160 (m-30) cc_final: 0.7822 (m-30) REVERT: B 271 GLU cc_start: 0.8326 (tt0) cc_final: 0.7791 (tm-30) REVERT: B 278 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7743 (tm130) REVERT: B 308 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7560 (mp0) REVERT: B 324 ASP cc_start: 0.8509 (t0) cc_final: 0.8295 (t0) REVERT: B 358 SER cc_start: 0.8915 (t) cc_final: 0.8614 (p) REVERT: B 435 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: B 437 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7099 (tmt-80) REVERT: B 449 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8042 (mm-30) outliers start: 104 outliers final: 59 residues processed: 633 average time/residue: 0.8854 time to fit residues: 624.7322 Evaluate side-chains 626 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 556 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 132 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 248 LYS 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 107 THR 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 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 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 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 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 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 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 530 THR 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 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 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: 0.9990 chunk 149 optimal weight: 0.0020 chunk 41 optimal weight: 0.4980 chunk 178 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 0.2980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 372 ASN A 488 HIS E 252 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS F 422 ASN F 488 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 = 0.3525 r_free = 0.3525 target = 0.111464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097894 restraints weight = 46296.337| |-----------------------------------------------------------------------------| 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: 4.80 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2083 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= 0.130 Angle : 0.588 9.870 35696 Z= 0.294 Chirality : 0.041 0.147 3961 Planarity : 0.005 0.054 4622 Dihedral : 9.460 93.458 3875 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 3.91 % Allowed : 20.25 % Favored : 75.84 % 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: 0.79 (0.16), residues: 3184 helix: 1.76 (0.14), residues: 1463 sheet: -0.73 (0.25), residues: 419 loop : -0.39 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 71 TYR 0.009 0.001 TYR C 356 PHE 0.027 0.001 PHE B 59 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 0.00306 / 0.13 (26118) covalent geometry : angle 0.58809 / 0.29 (35696) hydrogen bonds : bond 0.03557 / 2.37 ( 1160) hydrogen bonds : angle 4.44786 / 3.25 ( 3252) metal coordination : bond 0.00180 / 0.10 ( 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 669 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 567 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8343 (mtp) cc_final: 0.8119 (mtp) REVERT: C 199 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8336 (mtp180) REVERT: C 269 HIS cc_start: 0.7879 (m-70) cc_final: 0.7652 (m-70) REVERT: C 408 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7818 (mtt90) REVERT: C 601 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8391 (mp) REVERT: D 71 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7915 (mtm-85) REVERT: D 139 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6905 (ptt90) REVERT: D 203 GLU cc_start: 0.8392 (tp30) cc_final: 0.7793 (tp30) REVERT: D 221 GLU cc_start: 0.8495 (pp20) cc_final: 0.8039 (tm-30) REVERT: D 383 GLU cc_start: 0.8224 (tp30) cc_final: 0.7981 (mm-30) REVERT: D 443 MET cc_start: 0.7558 (mmm) cc_final: 0.7284 (mmm) REVERT: D 526 GLU cc_start: 0.8534 (mp0) cc_final: 0.8277 (mp0) REVERT: A 1 MET cc_start: 0.8014 (tpp) cc_final: 0.7381 (pp-130) REVERT: A 25 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8091 (mm-40) REVERT: A 29 GLU cc_start: 0.8147 (tt0) cc_final: 0.7549 (mm-30) REVERT: A 58 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7708 (mpp80) REVERT: A 89 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: A 113 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: A 139 ARG cc_start: 0.7544 (ptm160) cc_final: 0.7284 (ptm160) REVERT: A 140 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: A 142 SER cc_start: 0.8539 (t) cc_final: 0.8196 (p) REVERT: A 157 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8436 (mtm-85) REVERT: A 181 GLU cc_start: 0.8256 (tt0) cc_final: 0.8024 (tt0) REVERT: A 185 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 243 ASP cc_start: 0.8418 (t0) cc_final: 0.8087 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8475 (tp) cc_final: 0.8181 (tm) REVERT: A 385 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8210 (ttp80) REVERT: A 477 LYS cc_start: 0.8871 (tppt) cc_final: 0.8472 (mppt) REVERT: A 530 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8400 (p) REVERT: E 235 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7384 (mm) REVERT: E 279 GLU cc_start: 0.8730 (mm-30) cc_final: 0.7742 (tm-30) REVERT: E 342 ASP cc_start: 0.8693 (t0) cc_final: 0.8284 (t0) REVERT: E 449 GLU cc_start: 0.8689 (tp30) cc_final: 0.8293 (tp30) REVERT: E 534 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8473 (mmm-85) REVERT: E 600 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8264 (ttt90) REVERT: F 237 TRP cc_start: 0.8314 (t-100) cc_final: 0.7771 (t-100) REVERT: F 258 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7363 (tm-30) REVERT: F 271 GLU cc_start: 0.7627 (tp30) cc_final: 0.6951 (tp30) REVERT: F 275 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8425 (ttmm) REVERT: F 312 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7330 (mmm160) REVERT: F 315 ASP cc_start: 0.8757 (m-30) cc_final: 0.7844 (m-30) REVERT: F 324 ASP cc_start: 0.8209 (t0) cc_final: 0.7897 (t70) REVERT: F 348 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: F 383 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 418 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8091 (mt-10) REVERT: F 491 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8079 (mtt-85) REVERT: F 507 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8061 (mt-10) REVERT: F 525 GLN cc_start: 0.7906 (pm20) cc_final: 0.7486 (pp30) REVERT: F 534 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8411 (mtp85) REVERT: B 37 SER cc_start: 0.8748 (t) cc_final: 0.8534 (p) REVERT: B 154 ASN cc_start: 0.8617 (t0) cc_final: 0.8375 (t0) REVERT: B 184 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 271 GLU cc_start: 0.8333 (tt0) cc_final: 0.7783 (tm-30) REVERT: B 278 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7715 (tm130) REVERT: B 308 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7555 (mp0) REVERT: B 315 ASP cc_start: 0.8705 (m-30) cc_final: 0.8469 (m-30) REVERT: B 324 ASP cc_start: 0.8513 (t0) cc_final: 0.8293 (t0) REVERT: B 358 SER cc_start: 0.8908 (t) cc_final: 0.8600 (p) REVERT: B 435 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6800 (mm-30) REVERT: B 437 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7124 (tmt-80) REVERT: B 449 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8025 (mm-30) outliers start: 102 outliers final: 60 residues processed: 627 average time/residue: 0.8883 time to fit residues: 621.6852 Evaluate side-chains 625 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 553 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 284 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 107 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 196 MET 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 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 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 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 393 LEU 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 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 243 ASP 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 509 CYS Chi-restraints excluded: chain F residue 530 THR 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 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: 0.9980 chunk 167 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 249 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 372 ASN A 488 HIS E 252 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 GLN ** E 461 HIS ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097804 restraints weight = 46103.552| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.23 r_work: 0.3173 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26136 Z= 0.138 Angle : 0.606 11.287 35696 Z= 0.304 Chirality : 0.041 0.137 3961 Planarity : 0.005 0.070 4622 Dihedral : 9.283 93.386 3871 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 3.76 % Allowed : 21.59 % Favored : 74.65 % 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: 0.79 (0.16), residues: 3184 helix: 1.78 (0.14), residues: 1462 sheet: -0.79 (0.25), residues: 427 loop : -0.40 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 49 TYR 0.017 0.001 TYR D 50 PHE 0.022 0.001 PHE B 51 TRP 0.014 0.001 TRP D 167 HIS 0.008 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (26118) covalent geometry : angle 0.60602 / 0.30 (35696) hydrogen bonds : bond 0.03517 / 2.35 ( 1160) hydrogen bonds : angle 4.44223 / 3.24 ( 3252) metal coordination : bond 0.00194 / 0.12 ( 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 662 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 564 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8387 (mtp) cc_final: 0.8117 (mtp) REVERT: C 199 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8305 (mtp180) REVERT: C 258 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7785 (tm-30) REVERT: C 269 HIS cc_start: 0.7889 (m-70) cc_final: 0.7658 (m-70) REVERT: C 408 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7818 (mtt90) REVERT: C 601 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 71 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7885 (mtm-85) REVERT: D 139 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6831 (ppt170) REVERT: D 157 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7712 (ttm110) REVERT: D 203 GLU cc_start: 0.8393 (tp30) cc_final: 0.7788 (tp30) REVERT: D 221 GLU cc_start: 0.8483 (pp20) cc_final: 0.8026 (tm-30) REVERT: D 383 GLU cc_start: 0.8214 (tp30) cc_final: 0.7966 (mm-30) REVERT: D 443 MET cc_start: 0.7541 (mmm) cc_final: 0.7252 (mmm) REVERT: D 526 GLU cc_start: 0.8528 (mp0) cc_final: 0.8260 (mp0) REVERT: A 25 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8077 (mm-40) REVERT: A 29 GLU cc_start: 0.8112 (tt0) cc_final: 0.7549 (mm-30) REVERT: A 58 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7766 (mpp80) REVERT: A 89 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: A 113 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: A 139 ARG cc_start: 0.7515 (ptm160) cc_final: 0.7163 (ptm160) REVERT: A 140 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: A 142 SER cc_start: 0.8511 (t) cc_final: 0.8287 (p) REVERT: A 157 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8394 (mtm-85) REVERT: A 181 GLU cc_start: 0.8246 (tt0) cc_final: 0.8023 (tt0) REVERT: A 185 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 238 LEU cc_start: 0.8752 (tp) cc_final: 0.8394 (tt) REVERT: A 243 ASP cc_start: 0.8418 (t0) cc_final: 0.8119 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8474 (tp) cc_final: 0.8201 (tm) REVERT: A 385 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8206 (ttp80) REVERT: A 477 LYS cc_start: 0.8857 (tppt) cc_final: 0.8459 (mppt) REVERT: A 530 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8380 (p) REVERT: E 235 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7566 (mm) REVERT: E 279 GLU cc_start: 0.8718 (mm-30) cc_final: 0.7679 (tm-30) REVERT: E 342 ASP cc_start: 0.8697 (t0) cc_final: 0.8285 (t0) REVERT: E 348 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: E 449 GLU cc_start: 0.8639 (tp30) cc_final: 0.8229 (tp30) REVERT: E 600 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8321 (ttt90) REVERT: F 237 TRP cc_start: 0.8304 (t-100) cc_final: 0.7759 (t-100) REVERT: F 271 GLU cc_start: 0.7622 (tp30) cc_final: 0.6948 (tp30) REVERT: F 275 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8406 (ttmm) REVERT: F 312 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7378 (mmm160) REVERT: F 324 ASP cc_start: 0.8204 (t0) cc_final: 0.7902 (t70) REVERT: F 348 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: F 383 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 418 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 491 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8087 (mtt-85) REVERT: F 507 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8463 (mt-10) REVERT: F 521 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8990 (mm) REVERT: F 523 GLU cc_start: 0.7993 (tp30) cc_final: 0.7786 (tp30) REVERT: F 525 GLN cc_start: 0.7914 (pm20) cc_final: 0.7439 (pp30) REVERT: F 534 ARG cc_start: 0.8662 (mtp180) cc_final: 0.8448 (mtp85) REVERT: B 37 SER cc_start: 0.8737 (t) cc_final: 0.8515 (p) REVERT: B 154 ASN cc_start: 0.8633 (t0) cc_final: 0.8393 (t0) REVERT: B 184 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 271 GLU cc_start: 0.8336 (tt0) cc_final: 0.7779 (tm-30) REVERT: B 308 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7562 (mp0) REVERT: B 324 ASP cc_start: 0.8521 (t0) cc_final: 0.8313 (t0) REVERT: B 358 SER cc_start: 0.8906 (t) cc_final: 0.8606 (p) REVERT: B 418 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: B 449 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 477 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8648 (ttmm) REVERT: B 497 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8080 (ttp80) outliers start: 98 outliers final: 67 residues processed: 619 average time/residue: 0.8642 time to fit residues: 596.7926 Evaluate side-chains 644 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 563 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 284 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 107 THR Chi-restraints excluded: chain D residue 122 CYS 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 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 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 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 113 GLN Chi-restraints excluded: chain A residue 140 GLU 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 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 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 243 ASP 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 509 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 580 GLN 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 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 418 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 141 optimal weight: 0.7980 chunk 271 optimal weight: 0.0670 chunk 91 optimal weight: 0.7980 chunk 138 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 244 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 372 ASN D 473 GLN A 488 HIS E 252 GLN E 269 HIS E 282 ASN E 375 GLN ** E 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN F 234 HIS ** 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 = 0.3532 r_free = 0.3532 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098112 restraints weight = 46049.699| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.23 r_work: 0.3179 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2249 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= 0.125 Angle : 0.609 13.053 35696 Z= 0.304 Chirality : 0.041 0.148 3961 Planarity : 0.005 0.069 4622 Dihedral : 9.191 93.678 3871 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.72 % Allowed : 21.86 % Favored : 74.42 % 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: 1.82 (0.14), residues: 1460 sheet: -0.79 (0.25), residues: 428 loop : -0.37 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 49 TYR 0.019 0.001 TYR D 50 PHE 0.016 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 0.00297 / 0.13 (26118) covalent geometry : angle 0.60853 / 0.30 (35696) hydrogen bonds : bond 0.03367 / 2.25 ( 1160) hydrogen bonds : angle 4.40829 / 3.22 ( 3252) metal coordination : bond 0.00136 / 0.08 ( 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 671 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 574 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8221 (mtp) cc_final: 0.7967 (mtp) REVERT: C 258 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7755 (tm-30) REVERT: C 269 HIS cc_start: 0.7829 (m-70) cc_final: 0.7594 (m-70) REVERT: C 408 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7651 (mtt90) REVERT: C 601 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8407 (mp) REVERT: D 71 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: D 139 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6817 (ptt180) REVERT: D 157 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (ttm110) REVERT: D 203 GLU cc_start: 0.8382 (tp30) cc_final: 0.7713 (tp30) REVERT: D 221 GLU cc_start: 0.8524 (pp20) cc_final: 0.8073 (tm-30) REVERT: D 252 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: D 383 GLU cc_start: 0.8238 (tp30) cc_final: 0.7969 (mm-30) REVERT: D 443 MET cc_start: 0.7543 (mmm) cc_final: 0.7274 (mmm) REVERT: D 526 GLU cc_start: 0.8502 (mp0) cc_final: 0.8207 (mp0) REVERT: D 575 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: A 25 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8081 (mm-40) REVERT: A 29 GLU cc_start: 0.8166 (tt0) cc_final: 0.7706 (mm-30) REVERT: A 58 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7838 (mtm110) REVERT: A 89 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: A 113 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: A 130 GLU cc_start: 0.7680 (pt0) cc_final: 0.7338 (pm20) REVERT: A 140 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: A 142 SER cc_start: 0.8485 (t) cc_final: 0.8211 (p) REVERT: A 181 GLU cc_start: 0.8264 (tt0) cc_final: 0.8016 (tt0) REVERT: A 185 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 238 LEU cc_start: 0.8731 (tp) cc_final: 0.8396 (tt) REVERT: A 243 ASP cc_start: 0.8462 (t0) cc_final: 0.8157 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8431 (tp) cc_final: 0.8146 (tm) REVERT: A 385 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8236 (ttp80) REVERT: A 477 LYS cc_start: 0.8867 (tppt) cc_final: 0.8464 (mppt) REVERT: A 530 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (p) REVERT: E 235 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7562 (mm) REVERT: E 279 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7609 (tm-30) REVERT: E 312 ARG cc_start: 0.8128 (mmp-170) cc_final: 0.7631 (mmp-170) REVERT: E 342 ASP cc_start: 0.8683 (t0) cc_final: 0.8276 (t0) REVERT: E 348 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: E 449 GLU cc_start: 0.8646 (tp30) cc_final: 0.8130 (tp30) REVERT: E 600 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8334 (ttt90) REVERT: F 237 TRP cc_start: 0.8295 (t-100) cc_final: 0.7760 (t-100) REVERT: F 271 GLU cc_start: 0.7591 (tp30) cc_final: 0.6943 (tp30) REVERT: F 275 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8384 (ttmm) REVERT: F 312 ARG cc_start: 0.7937 (mmp80) cc_final: 0.7373 (mmm160) REVERT: F 324 ASP cc_start: 0.8183 (t0) cc_final: 0.7884 (t70) REVERT: F 348 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: F 383 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7423 (tm-30) REVERT: F 418 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8056 (mt-10) REVERT: F 461 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8183 (m90) REVERT: F 491 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8099 (mtt-85) REVERT: F 507 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8417 (mt-10) REVERT: F 521 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8952 (mm) REVERT: F 523 GLU cc_start: 0.7987 (tp30) cc_final: 0.7737 (tp30) REVERT: F 525 GLN cc_start: 0.7984 (pm20) cc_final: 0.7474 (pp30) REVERT: F 534 ARG cc_start: 0.8675 (mtp180) cc_final: 0.8453 (mtp85) REVERT: F 577 LEU cc_start: 0.8095 (mm) cc_final: 0.7880 (mt) REVERT: B 37 SER cc_start: 0.8797 (t) cc_final: 0.8560 (p) REVERT: B 69 ASP cc_start: 0.7400 (m-30) cc_final: 0.7173 (m-30) REVERT: B 154 ASN cc_start: 0.8675 (t0) cc_final: 0.8436 (t0) REVERT: B 184 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 236 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7893 (mtm110) REVERT: B 243 ASP cc_start: 0.8106 (p0) cc_final: 0.7719 (p0) REVERT: B 247 ASP cc_start: 0.8137 (m-30) cc_final: 0.7784 (m-30) REVERT: B 271 GLU cc_start: 0.8302 (tt0) cc_final: 0.7740 (tm-30) REVERT: B 308 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7560 (mp0) REVERT: B 324 ASP cc_start: 0.8525 (t0) cc_final: 0.8320 (t0) REVERT: B 358 SER cc_start: 0.8870 (t) cc_final: 0.8563 (p) REVERT: B 418 GLU cc_start: 0.8262 (pt0) cc_final: 0.8052 (pt0) REVERT: B 437 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7096 (tmt-80) REVERT: B 449 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8032 (mm-30) REVERT: B 477 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8626 (ttmm) REVERT: B 497 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8025 (ttp80) outliers start: 97 outliers final: 60 residues processed: 628 average time/residue: 0.6874 time to fit residues: 482.2984 Evaluate side-chains 633 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 557 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 248 LYS 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 252 GLN 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 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 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 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 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 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 243 ASP 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 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 521 LEU Chi-restraints excluded: chain F residue 530 THR 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 122 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 32 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 203 optimal weight: 0.0870 chunk 261 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 109 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 chunk 82 optimal weight: 0.0270 chunk 103 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 overall best weight: 0.2574 ------------------------------------------------------------------------------- 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 375 GLN ** E 461 HIS ** 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 96 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098508 restraints weight = 46141.389| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.24 r_work: 0.3189 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26136 Z= 0.119 Angle : 0.623 15.538 35696 Z= 0.311 Chirality : 0.041 0.160 3961 Planarity : 0.005 0.062 4622 Dihedral : 9.060 93.985 3869 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 3.49 % Allowed : 22.93 % Favored : 73.58 % 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: 0.89 (0.16), residues: 3184 helix: 1.85 (0.14), residues: 1466 sheet: -0.71 (0.25), residues: 426 loop : -0.36 (0.18), residues: 1292 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 0.013 0.001 PHE B 51 TRP 0.015 0.001 TRP A 86 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26118) covalent geometry : angle 0.62269 / 0.31 (35696) hydrogen bonds : bond 0.03244 / 2.18 ( 1160) hydrogen bonds : angle 4.37128 / 3.19 ( 3252) metal coordination : bond 0.00123 / 0.08 ( 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 651 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 560 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7427 (mmt-90) REVERT: C 69 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.6917 (OUTLIER) REVERT: C 77 MET cc_start: 0.8224 (mtp) cc_final: 0.7997 (mtp) REVERT: C 258 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7768 (tm-30) REVERT: C 269 HIS cc_start: 0.7821 (m-70) cc_final: 0.7581 (m-70) REVERT: C 601 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 71 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: D 139 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6865 (ptt90) REVERT: D 157 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7744 (ttm110) REVERT: D 203 GLU cc_start: 0.8348 (tp30) cc_final: 0.7700 (tp30) REVERT: D 221 GLU cc_start: 0.8532 (pp20) cc_final: 0.8088 (tm-30) REVERT: D 252 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: D 383 GLU cc_start: 0.8233 (tp30) cc_final: 0.7971 (mm-30) REVERT: D 443 MET cc_start: 0.7569 (mmm) cc_final: 0.7284 (mmm) REVERT: D 526 GLU cc_start: 0.8503 (mp0) cc_final: 0.8204 (mp0) REVERT: D 575 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: A 25 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8064 (mm-40) REVERT: A 29 GLU cc_start: 0.8184 (tt0) cc_final: 0.7729 (mm-30) REVERT: A 53 MET cc_start: 0.8129 (ptt) cc_final: 0.7801 (ppp) REVERT: A 58 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7803 (mtm110) REVERT: A 89 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: A 113 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: A 130 GLU cc_start: 0.7558 (pt0) cc_final: 0.7255 (pm20) REVERT: A 140 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6808 (mm-30) REVERT: A 181 GLU cc_start: 0.8246 (tt0) cc_final: 0.8005 (tt0) REVERT: A 185 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 238 LEU cc_start: 0.8692 (tp) cc_final: 0.8377 (tt) REVERT: A 243 ASP cc_start: 0.8462 (t0) cc_final: 0.8172 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8417 (tp) cc_final: 0.8145 (tm) REVERT: A 385 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8234 (ttp80) REVERT: A 477 LYS cc_start: 0.8843 (tppt) cc_final: 0.8432 (mppt) REVERT: A 530 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8381 (p) REVERT: E 278 GLN cc_start: 0.8559 (tt0) cc_final: 0.8255 (tt0) REVERT: E 279 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7635 (tm-30) REVERT: E 312 ARG cc_start: 0.8130 (mmp-170) cc_final: 0.7707 (mmp-170) REVERT: E 342 ASP cc_start: 0.8691 (t0) cc_final: 0.8274 (t0) REVERT: E 348 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: E 379 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: E 449 GLU cc_start: 0.8655 (tp30) cc_final: 0.8120 (tp30) REVERT: E 453 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8697 (mmm-85) REVERT: E 534 ARG cc_start: 0.8745 (mmt180) cc_final: 0.8515 (mmm-85) REVERT: E 600 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: F 237 TRP cc_start: 0.8297 (t-100) cc_final: 0.7677 (t-100) REVERT: F 240 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7911 (mp0) REVERT: F 258 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7410 (tm-30) REVERT: F 271 GLU cc_start: 0.7588 (tp30) cc_final: 0.6943 (tp30) REVERT: F 275 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8376 (ttmm) REVERT: F 312 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7303 (mmm160) REVERT: F 324 ASP cc_start: 0.8171 (t0) cc_final: 0.7866 (t70) REVERT: F 348 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: F 383 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7335 (tm-30) REVERT: F 449 GLU cc_start: 0.8543 (tp30) cc_final: 0.8127 (mm-30) REVERT: F 461 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8192 (m90) REVERT: F 469 GLU cc_start: 0.8292 (tp30) cc_final: 0.7897 (tm-30) REVERT: F 491 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8096 (mtt-85) REVERT: F 525 GLN cc_start: 0.7996 (pm20) cc_final: 0.7718 (pp30) REVERT: F 534 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8435 (mtp85) REVERT: F 575 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 37 SER cc_start: 0.8784 (t) cc_final: 0.8546 (p) REVERT: B 53 MET cc_start: 0.7847 (ppp) cc_final: 0.7390 (tmm) REVERT: B 77 MET cc_start: 0.8532 (ppp) cc_final: 0.8285 (tmt) REVERT: B 154 ASN cc_start: 0.8662 (t0) cc_final: 0.8436 (t0) REVERT: B 236 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7971 (mtm110) REVERT: B 271 GLU cc_start: 0.8303 (tt0) cc_final: 0.7741 (tm-30) REVERT: B 308 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7550 (mp0) REVERT: B 358 SER cc_start: 0.8867 (t) cc_final: 0.8563 (p) REVERT: B 437 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7092 (tmt-80) REVERT: B 449 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 91 outliers final: 61 residues processed: 612 average time/residue: 0.8954 time to fit residues: 611.1787 Evaluate side-chains 614 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 539 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 164 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 384 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 107 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 252 GLN 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 575 GLU Chi-restraints excluded: chain D residue 604 VAL 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 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 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 376 GLN Chi-restraints excluded: chain A residue 393 LEU 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 348 GLU Chi-restraints excluded: chain E residue 379 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 243 ASP 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 530 THR 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 122 CYS 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 272 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 302 optimal weight: 0.7980 chunk 200 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 169 GLN 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 376 GLN F 488 HIS F 580 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS 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 = 0.3524 r_free = 0.3524 target = 0.111144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097670 restraints weight = 46169.075| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.23 r_work: 0.3171 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26136 Z= 0.160 Angle : 0.654 17.963 35696 Z= 0.327 Chirality : 0.042 0.173 3961 Planarity : 0.005 0.063 4622 Dihedral : 9.020 92.993 3868 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 3.11 % Allowed : 23.96 % Favored : 72.93 % 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: 1.81 (0.14), residues: 1465 sheet: -0.78 (0.25), residues: 430 loop : -0.38 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 290 TYR 0.019 0.001 TYR D 50 PHE 0.028 0.001 PHE A 59 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 0.00387 / 0.16 (26118) covalent geometry : angle 0.65403 / 0.33 (35696) hydrogen bonds : bond 0.03530 / 2.36 ( 1160) hydrogen bonds : angle 4.42423 / 3.23 ( 3252) metal coordination : bond 0.00256 / 0.15 ( 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: 81 poor density : 559 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7510 (mmt-90) REVERT: C 164 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: C 199 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8244 (ttm-80) REVERT: C 258 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7794 (tm-30) REVERT: C 269 HIS cc_start: 0.7882 (m-70) cc_final: 0.7640 (m-70) REVERT: C 488 HIS cc_start: 0.8434 (m170) cc_final: 0.7863 (m-70) REVERT: C 601 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 71 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8019 (mtm-85) REVERT: D 139 ARG cc_start: 0.7307 (ttp80) cc_final: 0.6896 (ptt90) REVERT: D 157 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7794 (ttm110) REVERT: D 203 GLU cc_start: 0.8379 (tp30) cc_final: 0.7714 (tp30) REVERT: D 221 GLU cc_start: 0.8485 (pp20) cc_final: 0.8056 (tm-30) REVERT: D 252 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: D 383 GLU cc_start: 0.8218 (tp30) cc_final: 0.7852 (tp30) REVERT: D 443 MET cc_start: 0.7559 (mmm) cc_final: 0.7293 (mmm) REVERT: D 526 GLU cc_start: 0.8536 (mp0) cc_final: 0.8277 (mp0) REVERT: A 1 MET cc_start: 0.7882 (tpp) cc_final: 0.7181 (pp-130) REVERT: A 25 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8078 (mm-40) REVERT: A 29 GLU cc_start: 0.8165 (tt0) cc_final: 0.7684 (mm-30) REVERT: A 53 MET cc_start: 0.8134 (ptt) cc_final: 0.7797 (ppp) REVERT: A 58 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7688 (mtm110) REVERT: A 69 ASP cc_start: 0.7926 (t0) cc_final: 0.7617 (t0) REVERT: A 89 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: A 130 GLU cc_start: 0.7607 (pt0) cc_final: 0.7075 (pm20) REVERT: A 140 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: A 181 GLU cc_start: 0.8287 (tt0) cc_final: 0.8049 (tt0) REVERT: A 185 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 238 LEU cc_start: 0.8710 (tp) cc_final: 0.8391 (tt) REVERT: A 243 ASP cc_start: 0.8453 (t0) cc_final: 0.8171 (OUTLIER) REVERT: A 307 LEU cc_start: 0.8454 (tp) cc_final: 0.8180 (tm) REVERT: A 385 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8217 (ttp80) REVERT: A 477 LYS cc_start: 0.8877 (tppt) cc_final: 0.8472 (mppt) REVERT: A 530 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8422 (p) REVERT: E 278 GLN cc_start: 0.8564 (tt0) cc_final: 0.8260 (tt0) REVERT: E 279 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7646 (tm-30) REVERT: E 312 ARG cc_start: 0.8148 (mmp-170) cc_final: 0.7758 (mmp-170) REVERT: E 342 ASP cc_start: 0.8695 (t0) cc_final: 0.8277 (t0) REVERT: E 348 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: E 449 GLU cc_start: 0.8680 (tp30) cc_final: 0.8129 (tp30) REVERT: E 453 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8697 (mmm-85) REVERT: E 534 ARG cc_start: 0.8775 (mmt180) cc_final: 0.8553 (mmm-85) REVERT: E 600 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8208 (ttt90) REVERT: F 237 TRP cc_start: 0.8291 (t-100) cc_final: 0.7745 (t-100) REVERT: F 258 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7507 (tm-30) REVERT: F 271 GLU cc_start: 0.7613 (tp30) cc_final: 0.6963 (tp30) REVERT: F 275 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8394 (ttmm) REVERT: F 312 ARG cc_start: 0.7897 (mmp80) cc_final: 0.7310 (mmm160) REVERT: F 324 ASP cc_start: 0.8208 (t0) cc_final: 0.7888 (t70) REVERT: F 348 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: F 376 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: F 383 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7347 (tm-30) REVERT: F 473 GLN cc_start: 0.8791 (mm110) cc_final: 0.8461 (mp10) REVERT: F 491 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8089 (mtt-85) REVERT: F 507 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8420 (mt-10) REVERT: F 523 GLU cc_start: 0.7965 (tp30) cc_final: 0.7720 (tp30) REVERT: F 525 GLN cc_start: 0.8021 (pm20) cc_final: 0.7523 (pm20) REVERT: F 534 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8444 (mtp85) REVERT: F 575 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 37 SER cc_start: 0.8754 (t) cc_final: 0.8538 (p) REVERT: B 53 MET cc_start: 0.7823 (ppp) cc_final: 0.7422 (tmm) REVERT: B 106 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7493 (mmtt) REVERT: B 236 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7995 (mtm110) REVERT: B 271 GLU cc_start: 0.8305 (tt0) cc_final: 0.7774 (tm-30) REVERT: B 278 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 308 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7544 (mp0) REVERT: B 309 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7889 (ttp80) REVERT: B 358 SER cc_start: 0.8892 (t) cc_final: 0.8597 (p) REVERT: B 449 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8039 (mm-30) outliers start: 81 outliers final: 57 residues processed: 605 average time/residue: 0.9001 time to fit residues: 606.5804 Evaluate side-chains 622 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 553 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 199 ARG 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 122 CYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 252 GLN 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 572 THR Chi-restraints excluded: chain D residue 604 VAL 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 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 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 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 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 243 ASP Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 376 GLN 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 509 CYS Chi-restraints excluded: chain F residue 530 THR 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 122 CYS Chi-restraints excluded: chain B residue 154 ASN 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 22 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 200 optimal weight: 0.8980 chunk 172 optimal weight: 0.1980 chunk 82 optimal weight: 0.0870 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS C 282 ASN C 554 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 372 ASN A 89 GLN A 138 ASN 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 F 234 HIS F 376 GLN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098704 restraints weight = 46020.911| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.22 r_work: 0.3190 rms_B_bonded: 2.78 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: 0.8493 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26136 Z= 0.125 Angle : 0.644 18.177 35696 Z= 0.322 Chirality : 0.041 0.148 3961 Planarity : 0.005 0.064 4622 Dihedral : 8.980 93.411 3868 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 2.95 % Allowed : 24.08 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 3184 helix: 1.85 (0.14), residues: 1463 sheet: -0.68 (0.26), residues: 427 loop : -0.37 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 49 TYR 0.020 0.001 TYR D 50 PHE 0.045 0.001 PHE A 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 0.00296 / 0.13 (26118) covalent geometry : angle 0.64389 / 0.32 (35696) hydrogen bonds : bond 0.03328 / 2.23 ( 1160) hydrogen bonds : angle 4.38273 / 3.20 ( 3252) metal coordination : bond 0.00103 / 0.06 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11799.03 seconds wall clock time: 213 minutes 51.92 seconds (12831.92 seconds total)