Starting phenix.real_space_refine on Sun Jul 5 19:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1i_65544/07_2026/9w1i_65544.map" } resolution = 2.84 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= 0.006 sd= 0.040 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 36 5.49 5 Mg 6 5.21 5 S 124 5.16 5 C 18306 2.51 5 N 5320 2.21 5 O 5332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s 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: 29130 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4768 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 568} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4768 Classifications: {'peptide': 609} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 567} Chain: "D" Number of atoms: 4767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4767 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 568} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" 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: "Y" 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: "Z" 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: "F" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4743 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 567} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 4742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4742 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 566} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4748 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 566} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 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: "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} 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: "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: "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: "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} Time building chain proxies: 6.25, per 1000 atoms: 0.21 Number of scatterers: 29130 At special positions: 0 Unit cell: (96.928, 203.176, 217.156, 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 124 16.00 P 36 15.00 Mg 6 11.99 O 5332 8.00 N 5320 7.00 C 18306 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 260 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 461 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 262 " 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 260 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 262 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 461 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 262 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 260 " 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 " 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6840 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 14 sheets defined 51.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 39 through 52 removed outlier: 4.069A pdb=" N GLY A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.938A pdb=" N GLN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.976A pdb=" N ARG A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.281A pdb=" N ALA A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.654A pdb=" N HIS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (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: 3.806A 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 362 through 381 removed outlier: 3.625A pdb=" N THR A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.613A pdb=" N ARG A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.888A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.569A pdb=" N THR A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.124A 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 'B' and resid 13 through 19 Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.891A pdb=" N GLY B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.906A pdb=" N HIS B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.686A pdb=" N LEU B 172 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 217 removed outlier: 4.640A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.512A pdb=" N ALA B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.591A pdb=" N HIS B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.553A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (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 318 through 323 removed outlier: 3.694A pdb=" N LYS B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 342 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.937A pdb=" N ALA B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 444 through 455 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 468 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 532 through 539 Processing helix chain 'B' and resid 556 through 568 removed outlier: 4.197A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.015A 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 helix chain 'D' and resid 13 through 19 removed outlier: 3.580A pdb=" N GLU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 196 through 215 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 231 through 240 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: 3.550A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 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 381 Processing helix chain 'D' and resid 404 through 420 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 455 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 467 through 477 removed outlier: 3.738A pdb=" N ILE D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.581A pdb=" N THR D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 590 through 602 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 54 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 105 through 120 Processing helix chain 'F' and resid 143 through 153 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.705A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 215 Processing helix chain 'F' and resid 224 through 230 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.109A pdb=" N ALA F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.654A pdb=" N HIS F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 3.648A 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 306 through 314 removed outlier: 4.033A pdb=" N GLY F 314 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.784A 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 405 through 420 removed outlier: 3.815A pdb=" N GLU F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 455 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 467 through 477 removed outlier: 4.294A pdb=" N ILE F 471 " --> pdb=" O ASP F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 491 Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.572A pdb=" N THR F 564 " --> pdb=" O ASN F 560 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 4.075A 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 'E' and resid 13 through 19 Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 72 through 91 removed outlier: 3.803A pdb=" N HIS E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 120 Processing helix chain 'E' and resid 143 through 153 Processing helix chain 'E' and resid 167 through 172 removed outlier: 4.113A pdb=" N LEU E 172 " --> pdb=" O GLN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 197 through 215 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.518A 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 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.594A pdb=" N HIS E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU E 279 " --> pdb=" O LYS E 275 " (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 324 through 342 Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 362 through 381 removed outlier: 3.584A pdb=" N THR E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 420 removed outlier: 4.179A pdb=" N GLU E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS E 419 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 444 through 455 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 468 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 556 through 568 removed outlier: 4.323A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 4.022A 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 'C' and resid 13 through 19 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 71 through 91 removed outlier: 3.976A pdb=" N ASP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 105 through 120 Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.844A pdb=" N LEU C 172 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 197 through 216 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 239 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 270 through 279 removed outlier: 3.751A 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 306 through 313 Processing helix chain 'C' and resid 324 through 341 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 381 removed outlier: 3.500A pdb=" N THR C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 436 through 443 removed outlier: 4.264A pdb=" N ARG C 440 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA C 441 " --> pdb=" O THR C 438 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA C 442 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 443 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 455 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 468 through 477 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: 4.080A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 4.027A 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 sheet with id=AA1, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.730A pdb=" N GLU A 123 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 7 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 4 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU A 33 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS A 6 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 35 " --> pdb=" O CYS A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 262 removed outlier: 6.034A pdb=" N LYS A 256 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 346 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS A 260 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A 350 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS A 262 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 388 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 426 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 391 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 428 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 427 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR A 459 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 429 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 164 removed outlier: 6.439A pdb=" N VAL B 124 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS B 122 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG B 97 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE B 125 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 127 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 3 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS B 100 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 5 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N HIS B 189 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 61 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 191 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG B 63 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 262 removed outlier: 4.586A pdb=" N VAL B 257 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU B 348 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU B 259 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 350 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 261 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 345 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASN B 390 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 347 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 392 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 349 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B 394 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS B 351 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 11.741A pdb=" N VAL B 389 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N GLY B 428 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 391 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASP B 430 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 393 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 457 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 483 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 156 through 164 removed outlier: 6.465A pdb=" N VAL D 124 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N CYS D 122 " --> pdb=" O PRO D 163 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG D 97 " --> pdb=" O CYS D 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL D 124 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 99 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS D 126 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 30 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER D 62 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 32 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL D 64 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR D 34 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N HIS D 189 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 61 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 191 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG D 63 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 190 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 256 through 262 removed outlier: 6.125A pdb=" N LYS D 256 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR D 346 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS D 260 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG D 350 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N HIS D 262 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 426 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 391 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY D 428 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 457 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY D 433 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU D 483 " --> pdb=" O GLU D 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 97 through 100 removed outlier: 6.698A pdb=" N ILE F 3 " --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N CYS F 100 " --> pdb=" O ILE F 3 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU F 5 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL F 30 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER F 62 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL F 32 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL F 64 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR F 34 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS F 189 " --> pdb=" O PHE F 59 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE F 61 " --> pdb=" O HIS F 189 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL F 191 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG F 63 " --> pdb=" O VAL F 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 121 through 129 removed outlier: 7.163A pdb=" N CYS F 122 " --> pdb=" O PRO F 163 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 124 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 256 through 262 removed outlier: 4.694A pdb=" N VAL F 257 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU F 348 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU F 259 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG F 350 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS F 261 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA F 345 " --> pdb=" O HIS F 388 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASN F 390 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA F 347 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU F 392 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE F 349 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR F 394 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS F 351 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR F 396 " --> pdb=" O CYS F 351 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL F 426 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU F 391 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY F 428 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL F 427 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR F 459 " --> pdb=" O VAL F 427 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 429 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS F 461 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU F 431 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU F 483 " --> pdb=" O GLU F 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.863A pdb=" N SER E 7 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR E 35 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL E 30 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER E 62 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL E 32 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL E 64 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR E 34 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 256 through 262 removed outlier: 5.973A pdb=" N LYS E 256 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR E 346 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS E 260 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG E 350 " --> pdb=" O HIS E 260 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS E 262 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E 388 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL E 427 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR E 459 " --> pdb=" O VAL E 427 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 429 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.956A pdb=" N ARG C 97 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE C 125 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE C 99 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL C 127 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU C 101 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N CYS C 129 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 13.334A pdb=" N GLY C 103 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER C 7 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA C 102 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 256 through 262 removed outlier: 5.993A pdb=" N LYS C 256 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 346 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N HIS C 260 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG C 350 " --> pdb=" O HIS C 260 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS C 262 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 388 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 426 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C 391 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 428 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL C 427 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR C 459 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 429 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS C 461 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU C 431 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 506 " --> pdb=" O THR C 544 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3726 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: 5.98 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9885 1.34 - 1.46: 5012 1.46 - 1.58: 14765 1.58 - 1.69: 61 1.69 - 1.81: 176 Bond restraints: 29899 Sorted by residual: bond pdb=" CA SER A 352 " pdb=" CB SER A 352 " ideal model delta sigma weight residual 1.530 1.492 0.037 1.32e-02 5.74e+03 7.90e+00 bond pdb=" N ASN A 317 " pdb=" CA ASN A 317 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.19e-02 7.06e+03 7.40e+00 bond pdb=" N PHE A 266 " pdb=" CA PHE A 266 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.22e-02 6.72e+03 6.51e+00 bond pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" N ASP A 315 " pdb=" CA ASP A 315 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.26e-02 6.30e+03 6.36e+00 ... (remaining 29894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 40455 2.46 - 4.92: 367 4.92 - 7.39: 41 7.39 - 9.85: 4 9.85 - 12.31: 1 Bond angle restraints: 40868 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 127.56 12.31 1.00e+00 1.00e+00 1.52e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 131.59 8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 134.59 5.28 1.00e+00 1.00e+00 2.79e+01 angle pdb=" C2 A Y 2 " pdb=" N3 A Y 2 " pdb=" C4 A Y 2 " ideal model delta sigma weight residual 110.60 113.16 -2.56 5.00e-01 4.00e+00 2.62e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 132.00 4.83 1.00e+00 1.00e+00 2.33e+01 ... (remaining 40863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 17738 35.08 - 70.17: 244 70.17 - 105.25: 14 105.25 - 140.33: 0 140.33 - 175.42: 1 Dihedral angle restraints: 17997 sinusoidal: 7449 harmonic: 10548 Sorted by residual: dihedral pdb=" CA ALA D 462 " pdb=" C ALA D 462 " pdb=" N GLY D 463 " pdb=" CA GLY D 463 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA VAL B 8 " pdb=" C VAL B 8 " pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CD ARG A 157 " pdb=" NE ARG A 157 " pdb=" CZ ARG A 157 " pdb=" NH1 ARG A 157 " ideal model delta sinusoidal sigma weight residual 0.00 -41.47 41.47 1 1.00e+01 1.00e-02 2.41e+01 ... (remaining 17994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4411 0.104 - 0.208: 100 0.208 - 0.312: 9 0.312 - 0.416: 2 0.416 - 0.520: 4 Chirality restraints: 4526 Sorted by residual: chirality pdb=" P A X 1 " pdb=" OP1 A X 1 " pdb=" OP2 A X 1 " pdb=" O5' A X 1 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P A X 6 " pdb=" OP1 A X 6 " pdb=" OP2 A X 6 " pdb=" O5' A X 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" P A X 5 " pdb=" OP1 A X 5 " pdb=" OP2 A X 5 " pdb=" O5' A X 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 4523 not shown) Planarity restraints: 5278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 157 " -0.711 9.50e-02 1.11e+02 3.19e-01 6.20e+01 pdb=" NE ARG A 157 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 157 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 157 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 157 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 56 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.42e+00 pdb=" N PRO F 57 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 56 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO C 57 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.037 5.00e-02 4.00e+02 ... (remaining 5275 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 251 2.58 - 3.16: 24646 3.16 - 3.74: 46775 3.74 - 4.32: 64246 4.32 - 4.90: 108970 Nonbonded interactions: 244888 Sorted by model distance: nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 702 " model vdw 1.999 2.230 nonbonded pdb=" OD1 ASP E 548 " pdb="ZN ZN E 702 " model vdw 2.004 2.230 nonbonded pdb=" OD1 ASP C 548 " pdb="ZN ZN C 702 " model vdw 2.006 2.230 nonbonded pdb=" OD1 ASP F 548 " pdb="ZN ZN F 702 " model vdw 2.010 2.230 nonbonded pdb=" OD1 ASP D 548 " pdb="ZN ZN D 702 " model vdw 2.029 2.230 ... (remaining 244883 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 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 433 or (resid 434 throu \ gh 435 and (name N or name CA or name C or name O or name CB )) or resid 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 438 \ through 463 or (resid 464 and (name N or name CA or name C or name O or name CB \ )) or resid 465 through 608 or resid 701 through 703)) selection = (chain 'B' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 92 or (resid 93 through \ 95 and (name N or name CA or name C or name O or name CB )) or resid 96 through \ 433 or (resid 434 through 435 and (name N or name CA or name C or name O or nam \ e CB )) or resid 436 or (resid 437 and (name N or name CA or name C or name O or \ name CB )) or resid 438 through 463 or (resid 464 and (name N or name CA or nam \ e C or name O or name CB )) or resid 465 through 608 or resid 701 through 703)) selection = (chain 'C' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 92 or (resid 93 through \ 95 and (name N or name CA or name C or name O or name CB )) or resid 96 through \ 433 or (resid 434 through 435 and (name N or name CA or name C or name O or nam \ e CB )) or resid 436 through 463 or (resid 464 and (name N or name CA or name C \ or name O or name CB )) or resid 465 through 703)) selection = (chain 'D' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 through 92 or (resid 93 through \ 95 and (name N or name CA or name C or name O or name CB )) or resid 96 through \ 433 or (resid 434 through 435 and (name N or name CA or name C or name O or nam \ e CB )) or resid 436 or (resid 437 and (name N or name CA or name C or name O or \ name CB )) or resid 438 through 608 or resid 701 through 703)) selection = (chain 'E' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 92 or (resid 93 through 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 434 or (resi \ d 435 and (name N or name CA or name C or name O or name CB )) or resid 436 thro \ ugh 463 or (resid 464 and (name N or name CA or name C or name O or name CB )) o \ r resid 465 through 703)) selection = (chain 'F' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 92 or (resid 93 through 95 and (name N or name CA \ or name C or name O or name CB )) or resid 96 through 434 or (resid 435 and (na \ me N or name CA or name C or name O or name CB )) or resid 436 through 463 or (r \ esid 464 and (name N or name CA or name C or name O or name CB )) or resid 465 t \ hrough 608 or resid 701 through 703)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.520 Find NCS groups from input model: 1.010 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: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 29917 Z= 0.219 Angle : 0.562 12.312 40868 Z= 0.315 Chirality : 0.046 0.520 4526 Planarity : 0.006 0.319 5278 Dihedral : 12.110 175.418 11157 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.02 % Favored : 94.78 % Rotamer: Outliers : 1.11 % Allowed : 6.22 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.80 (0.14), residues: 3642 helix: 1.93 (0.13), residues: 1597 sheet: -0.62 (0.23), residues: 573 loop : -0.50 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.013 0.001 TYR F 98 PHE 0.009 0.001 PHE A 125 TRP 0.014 0.001 TRP B 167 HIS 0.006 0.001 HIS D 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (29899) covalent geometry : angle 0.56213 / 0.31 (40868) hydrogen bonds : bond 0.15183 / 10.07 ( 1317) hydrogen bonds : angle 5.82782 / 4.23 ( 3726) metal coordination : bond 0.07418 / 3.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 673 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8681 (mp) cc_final: 0.8183 (mt) REVERT: A 51 PHE cc_start: 0.8508 (m-80) cc_final: 0.8276 (m-80) REVERT: A 165 PRO cc_start: 0.8864 (Cg_exo) cc_final: 0.8652 (Cg_endo) REVERT: B 22 LEU cc_start: 0.8524 (mt) cc_final: 0.8172 (mp) REVERT: B 210 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7983 (mtp180) REVERT: B 329 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7900 (ttt90) REVERT: D 25 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: D 524 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 51 PHE cc_start: 0.7971 (m-10) cc_final: 0.7645 (m-10) REVERT: F 203 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7178 (tm-30) REVERT: E 1 MET cc_start: 0.8012 (ttm) cc_final: 0.7721 (ttm) REVERT: E 51 PHE cc_start: 0.8569 (m-10) cc_final: 0.8238 (m-10) REVERT: E 207 GLU cc_start: 0.7964 (tt0) cc_final: 0.7738 (tt0) REVERT: C 19 MET cc_start: 0.7905 (mtm) cc_final: 0.7704 (mtm) REVERT: C 136 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6900 (tm-30) REVERT: C 220 SER cc_start: 0.8664 (p) cc_final: 0.8452 (p) REVERT: C 385 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8264 (mtp-110) REVERT: C 405 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7969 (mtt90) outliers start: 33 outliers final: 7 residues processed: 698 average time/residue: 0.8830 time to fit residues: 696.8375 Evaluate side-chains 541 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 532 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0030 chunk 298 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 89 GLN A 136 GLN A 169 GLN A 473 GLN A 515 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 252 GLN B 376 GLN B 390 ASN B 485 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 331 GLN D 513 ASN D 590 ASN D 591 GLN F 76 HIS F 169 GLN F 473 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN E 485 HIS E 549 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 546 ASN C 549 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083395 restraints weight = 56699.657| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3136 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29917 Z= 0.149 Angle : 0.624 12.319 40868 Z= 0.312 Chirality : 0.042 0.193 4526 Planarity : 0.006 0.083 5278 Dihedral : 9.507 170.853 4425 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 3.03 % Allowed : 13.28 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.98 (0.15), residues: 3642 helix: 2.01 (0.13), residues: 1617 sheet: -0.61 (0.23), residues: 562 loop : -0.31 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 157 TYR 0.012 0.001 TYR F 50 PHE 0.024 0.001 PHE E 59 TRP 0.015 0.001 TRP D 167 HIS 0.005 0.001 HIS E 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (29899) covalent geometry : angle 0.62411 / 0.31 (40868) hydrogen bonds : bond 0.04374 / 2.98 ( 1317) hydrogen bonds : angle 4.86404 / 3.53 ( 3726) metal coordination : bond 0.00911 / 0.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 549 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7738 (mtm110) cc_final: 0.6636 (mtm110) REVERT: A 10 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 22 LEU cc_start: 0.8618 (mp) cc_final: 0.8287 (mp) REVERT: A 29 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 71 ARG cc_start: 0.7712 (pmt170) cc_final: 0.7467 (pmt170) REVERT: A 85 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7599 (mtt180) REVERT: A 183 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (p) REVERT: B 22 LEU cc_start: 0.8574 (mt) cc_final: 0.8271 (mp) REVERT: B 50 TYR cc_start: 0.8562 (t80) cc_final: 0.8338 (t80) REVERT: B 71 ARG cc_start: 0.7643 (pmm-80) cc_final: 0.7366 (pmm-80) REVERT: B 93 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5870 (pp30) REVERT: B 96 HIS cc_start: 0.7899 (m170) cc_final: 0.7107 (m90) REVERT: B 329 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8047 (ttt90) REVERT: B 449 GLU cc_start: 0.8176 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 533 LEU cc_start: 0.8294 (tp) cc_final: 0.7967 (tt) REVERT: D 22 LEU cc_start: 0.8567 (mt) cc_final: 0.7728 (mm) REVERT: D 25 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: D 71 ARG cc_start: 0.8192 (ptp-110) cc_final: 0.7698 (mtm-85) REVERT: D 303 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8385 (mp0) REVERT: D 528 SER cc_start: 0.8947 (t) cc_final: 0.8674 (t) REVERT: D 529 GLU cc_start: 0.8165 (mp0) cc_final: 0.7950 (mp0) REVERT: F 8 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8171 (m) REVERT: F 25 GLN cc_start: 0.8103 (tp40) cc_final: 0.7776 (tp-100) REVERT: F 39 LYS cc_start: 0.7781 (tptp) cc_final: 0.7477 (tptp) REVERT: F 51 PHE cc_start: 0.8402 (m-10) cc_final: 0.8141 (m-80) REVERT: F 59 PHE cc_start: 0.7448 (m-10) cc_final: 0.7186 (m-10) REVERT: F 71 ARG cc_start: 0.7562 (mtm110) cc_final: 0.7218 (mtm110) REVERT: F 203 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7319 (tm-30) REVERT: F 240 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: F 243 ASP cc_start: 0.8008 (t0) cc_final: 0.7705 (t70) REVERT: F 275 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7945 (mtmt) REVERT: F 385 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7791 (mtm-85) REVERT: F 526 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7312 (tm-30) REVERT: F 528 SER cc_start: 0.8852 (m) cc_final: 0.8558 (p) REVERT: E 12 TRP cc_start: 0.8843 (p-90) cc_final: 0.8454 (p-90) REVERT: E 27 PHE cc_start: 0.7868 (m-10) cc_final: 0.7618 (m-10) REVERT: E 59 PHE cc_start: 0.8280 (m-80) cc_final: 0.7833 (m-80) REVERT: E 130 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7016 (mt-10) REVERT: E 206 LEU cc_start: 0.8636 (mm) cc_final: 0.8326 (mt) REVERT: E 517 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8671 (mtpm) REVERT: E 591 GLN cc_start: 0.8285 (mt0) cc_final: 0.8058 (mp10) REVERT: C 96 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7431 (p90) REVERT: C 139 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7392 (ptp90) REVERT: C 405 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8062 (mtt90) REVERT: C 529 GLU cc_start: 0.8235 (mp0) cc_final: 0.7909 (mp0) outliers start: 90 outliers final: 26 residues processed: 594 average time/residue: 0.9164 time to fit residues: 612.3203 Evaluate side-chains 544 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 510 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 186 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS A 169 GLN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS D 154 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 169 GLN F 546 ASN E 488 HIS E 546 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 113 GLN C 154 ASN C 282 ASN C 488 HIS C 525 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080837 restraints weight = 56877.888| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.26 r_work: 0.3088 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29917 Z= 0.246 Angle : 0.638 9.033 40868 Z= 0.321 Chirality : 0.044 0.200 4526 Planarity : 0.006 0.125 5278 Dihedral : 9.275 169.258 4416 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.41 % Rotamer: Outliers : 3.03 % Allowed : 15.16 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3642 helix: 1.82 (0.13), residues: 1621 sheet: -0.69 (0.22), residues: 583 loop : -0.45 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 157 TYR 0.023 0.002 TYR D 50 PHE 0.024 0.002 PHE E 133 TRP 0.025 0.002 TRP E 190 HIS 0.007 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (29899) covalent geometry : angle 0.63781 / 0.32 (40868) hydrogen bonds : bond 0.04523 / 3.08 ( 1317) hydrogen bonds : angle 4.75587 / 3.46 ( 3726) metal coordination : bond 0.00418 / 0.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7759 (mtm110) cc_final: 0.6683 (mtm110) REVERT: A 10 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 29 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7473 (mp0) REVERT: A 71 ARG cc_start: 0.7751 (pmt170) cc_final: 0.7491 (pmt170) REVERT: A 85 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7164 (mmt-90) REVERT: A 184 LEU cc_start: 0.7907 (mt) cc_final: 0.7686 (tm) REVERT: A 279 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: A 575 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: B 22 LEU cc_start: 0.8445 (mt) cc_final: 0.8216 (mt) REVERT: B 71 ARG cc_start: 0.7648 (pmm-80) cc_final: 0.7305 (pmm-80) REVERT: B 93 GLN cc_start: 0.6198 (pm20) cc_final: 0.5874 (pp30) REVERT: B 96 HIS cc_start: 0.7987 (m170) cc_final: 0.7178 (m90) REVERT: B 329 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8129 (ttt-90) REVERT: D 22 LEU cc_start: 0.8682 (mt) cc_final: 0.7902 (mm) REVERT: D 25 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: D 73 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6953 (mm-30) REVERT: D 77 MET cc_start: 0.8188 (mtp) cc_final: 0.7790 (ttm) REVERT: D 157 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7224 (ttp80) REVERT: D 303 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8416 (mp0) REVERT: D 385 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8478 (mtm-85) REVERT: D 524 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: D 590 ASN cc_start: 0.8815 (p0) cc_final: 0.8574 (p0) REVERT: F 8 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8246 (m) REVERT: F 19 MET cc_start: 0.8231 (mtp) cc_final: 0.7828 (mtm) REVERT: F 22 LEU cc_start: 0.9067 (mt) cc_final: 0.8624 (mp) REVERT: F 39 LYS cc_start: 0.7908 (tptp) cc_final: 0.7619 (tptp) REVERT: F 71 ARG cc_start: 0.7622 (mtm110) cc_final: 0.7265 (mtm110) REVERT: F 77 MET cc_start: 0.8723 (ttm) cc_final: 0.8321 (mtp) REVERT: F 164 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6752 (pp20) REVERT: F 203 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7322 (tm-30) REVERT: F 243 ASP cc_start: 0.8156 (t0) cc_final: 0.7819 (t70) REVERT: F 275 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8032 (mtmt) REVERT: F 528 SER cc_start: 0.8871 (m) cc_final: 0.8584 (p) REVERT: E 59 PHE cc_start: 0.8415 (m-80) cc_final: 0.8038 (m-10) REVERT: E 130 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 206 LEU cc_start: 0.8740 (mm) cc_final: 0.8396 (mt) REVERT: E 236 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7875 (ttp80) REVERT: E 517 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8725 (mtpm) REVERT: E 591 GLN cc_start: 0.8329 (mt0) cc_final: 0.8089 (mp10) REVERT: C 29 GLU cc_start: 0.8136 (tt0) cc_final: 0.7922 (tt0) REVERT: C 49 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (ttm-80) REVERT: C 160 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8110 (ttp-110) REVERT: C 196 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: C 279 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: C 302 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8559 (mp0) REVERT: C 398 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 405 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8121 (mtt90) REVERT: C 529 GLU cc_start: 0.8211 (mp0) cc_final: 0.7894 (mp0) outliers start: 90 outliers final: 39 residues processed: 573 average time/residue: 0.9032 time to fit residues: 581.5151 Evaluate side-chains 549 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 497 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 169 GLN E 488 HIS ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 525 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080860 restraints weight = 56553.845| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.25 r_work: 0.3090 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29917 Z= 0.215 Angle : 0.625 9.225 40868 Z= 0.313 Chirality : 0.044 0.197 4526 Planarity : 0.006 0.105 5278 Dihedral : 9.160 168.373 4413 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.42 % Favored : 95.44 % Rotamer: Outliers : 3.16 % Allowed : 16.24 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.73 (0.14), residues: 3642 helix: 1.80 (0.13), residues: 1617 sheet: -0.72 (0.22), residues: 569 loop : -0.45 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 157 TYR 0.019 0.002 TYR A 50 PHE 0.024 0.001 PHE F 59 TRP 0.015 0.001 TRP B 167 HIS 0.009 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (29899) covalent geometry : angle 0.62463 / 0.31 (40868) hydrogen bonds : bond 0.04243 / 2.89 ( 1317) hydrogen bonds : angle 4.66062 / 3.39 ( 3726) metal coordination : bond 0.00440 / 0.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 508 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7509 (mtm110) REVERT: A 10 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (p) REVERT: A 71 ARG cc_start: 0.7805 (pmt170) cc_final: 0.7505 (pmt170) REVERT: A 85 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7204 (mmt-90) REVERT: A 279 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: A 575 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: B 71 ARG cc_start: 0.7651 (pmm-80) cc_final: 0.7294 (pmm-80) REVERT: B 93 GLN cc_start: 0.6145 (pm20) cc_final: 0.5864 (pp30) REVERT: B 96 HIS cc_start: 0.7931 (m170) cc_final: 0.7129 (m90) REVERT: B 139 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7499 (ptp90) REVERT: B 154 ASN cc_start: 0.8547 (t0) cc_final: 0.8028 (t0) REVERT: B 329 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8080 (ttt-90) REVERT: B 529 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: D 2 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: D 22 LEU cc_start: 0.8703 (mt) cc_final: 0.7908 (mm) REVERT: D 25 GLN cc_start: 0.8105 (pm20) cc_final: 0.7903 (pm20) REVERT: D 39 LYS cc_start: 0.8518 (tppt) cc_final: 0.8263 (tptp) REVERT: D 77 MET cc_start: 0.8171 (mtp) cc_final: 0.7948 (ptm) REVERT: D 157 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7129 (ttp80) REVERT: D 200 GLN cc_start: 0.8304 (pt0) cc_final: 0.8078 (pm20) REVERT: D 385 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8439 (mtm-85) REVERT: D 524 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: F 8 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (m) REVERT: F 39 LYS cc_start: 0.7938 (tptp) cc_final: 0.7602 (tptp) REVERT: F 71 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7271 (mtm110) REVERT: F 77 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: F 164 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6726 (pp20) REVERT: F 196 MET cc_start: 0.8643 (mtp) cc_final: 0.8438 (mtp) REVERT: F 203 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7363 (tm-30) REVERT: F 243 ASP cc_start: 0.8156 (t0) cc_final: 0.7820 (t70) REVERT: F 275 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8029 (mtmt) REVERT: F 528 SER cc_start: 0.8844 (m) cc_final: 0.8476 (p) REVERT: F 529 GLU cc_start: 0.8506 (mp0) cc_final: 0.8267 (mp0) REVERT: E 27 PHE cc_start: 0.7948 (m-10) cc_final: 0.7660 (m-10) REVERT: E 28 ASP cc_start: 0.7897 (t0) cc_final: 0.7575 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8403 (m-80) cc_final: 0.8047 (m-10) REVERT: E 130 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 206 LEU cc_start: 0.8681 (mm) cc_final: 0.8356 (mt) REVERT: E 236 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7872 (ttp80) REVERT: E 246 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: E 517 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8763 (mtpt) REVERT: E 591 GLN cc_start: 0.8309 (mt0) cc_final: 0.8082 (mp10) REVERT: C 50 TYR cc_start: 0.8737 (t80) cc_final: 0.8521 (t80) REVERT: C 53 MET cc_start: 0.8094 (ppp) cc_final: 0.7892 (ppp) REVERT: C 196 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: C 279 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: C 405 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8133 (mtt90) REVERT: C 529 GLU cc_start: 0.8216 (mp0) cc_final: 0.7883 (mp0) outliers start: 94 outliers final: 41 residues processed: 567 average time/residue: 0.8836 time to fit residues: 563.0447 Evaluate side-chains 546 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 492 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 336 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 342 optimal weight: 0.8980 chunk 138 optimal weight: 0.0870 chunk 175 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 96 HIS E 488 HIS E 546 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 488 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081428 restraints weight = 57555.107| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.29 r_work: 0.3099 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29917 Z= 0.151 Angle : 0.603 9.784 40868 Z= 0.302 Chirality : 0.042 0.192 4526 Planarity : 0.005 0.090 5278 Dihedral : 8.976 167.323 4410 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 3.13 % Allowed : 17.38 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.81 (0.15), residues: 3642 helix: 1.85 (0.13), residues: 1625 sheet: -0.68 (0.22), residues: 569 loop : -0.40 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 157 TYR 0.020 0.001 TYR A 50 PHE 0.034 0.001 PHE F 59 TRP 0.014 0.001 TRP B 167 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (29899) covalent geometry : angle 0.60329 / 0.30 (40868) hydrogen bonds : bond 0.03832 / 2.61 ( 1317) hydrogen bonds : angle 4.53219 / 3.30 ( 3726) metal coordination : bond 0.00223 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 509 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7452 (mtm110) REVERT: A 10 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 71 ARG cc_start: 0.7839 (pmt170) cc_final: 0.7506 (pmt170) REVERT: A 85 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7597 (mtp85) REVERT: A 183 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (p) REVERT: A 279 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: A 575 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: B 71 ARG cc_start: 0.7616 (pmm-80) cc_final: 0.7270 (pmm-80) REVERT: B 93 GLN cc_start: 0.6154 (pm20) cc_final: 0.5752 (pp30) REVERT: B 96 HIS cc_start: 0.7911 (m170) cc_final: 0.7133 (m90) REVERT: B 106 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7663 (mmtp) REVERT: B 139 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7729 (ptt90) REVERT: B 154 ASN cc_start: 0.8502 (t0) cc_final: 0.8019 (t0) REVERT: B 329 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8087 (ttt-90) REVERT: B 529 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: D 2 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: D 22 LEU cc_start: 0.8724 (mt) cc_final: 0.7917 (mm) REVERT: D 39 LYS cc_start: 0.8479 (tppt) cc_final: 0.8210 (tptp) REVERT: D 157 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6311 (ttp80) REVERT: D 491 ARG cc_start: 0.8575 (mmt90) cc_final: 0.8268 (mtt90) REVERT: D 524 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: F 8 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8321 (m) REVERT: F 19 MET cc_start: 0.8189 (mtp) cc_final: 0.7801 (mtm) REVERT: F 22 LEU cc_start: 0.9046 (mp) cc_final: 0.8740 (mt) REVERT: F 39 LYS cc_start: 0.7906 (tptp) cc_final: 0.7540 (tptp) REVERT: F 71 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7247 (mtm110) REVERT: F 77 MET cc_start: 0.8635 (ttm) cc_final: 0.8125 (mtp) REVERT: F 164 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: F 199 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.8051 (mmm160) REVERT: F 203 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7352 (tm-30) REVERT: F 243 ASP cc_start: 0.8193 (t0) cc_final: 0.7829 (t70) REVERT: F 275 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8002 (mtmt) REVERT: F 528 SER cc_start: 0.8810 (m) cc_final: 0.8423 (p) REVERT: F 529 GLU cc_start: 0.8484 (mp0) cc_final: 0.8243 (mp0) REVERT: E 59 PHE cc_start: 0.8334 (m-80) cc_final: 0.7949 (m-10) REVERT: E 130 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7410 (mt-10) REVERT: E 206 LEU cc_start: 0.8712 (mm) cc_final: 0.8395 (mt) REVERT: E 236 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7891 (ttp80) REVERT: E 246 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: E 349 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8601 (mp) REVERT: E 517 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8759 (mtpt) REVERT: E 591 GLN cc_start: 0.8357 (mt0) cc_final: 0.8096 (mp10) REVERT: C 77 MET cc_start: 0.8442 (mtp) cc_final: 0.8176 (mmt) REVERT: C 78 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8183 (pp) REVERT: C 113 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: C 279 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: C 405 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8124 (mtt90) REVERT: C 529 GLU cc_start: 0.8212 (mp0) cc_final: 0.7995 (mp0) outliers start: 93 outliers final: 39 residues processed: 569 average time/residue: 0.9064 time to fit residues: 578.5399 Evaluate side-chains 546 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 490 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.0470 chunk 349 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 150 optimal weight: 0.2980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 269 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 20 GLN F 96 HIS F 136 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 HIS ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 513 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082115 restraints weight = 57515.726| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.29 r_work: 0.3113 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29917 Z= 0.130 Angle : 0.601 10.099 40868 Z= 0.303 Chirality : 0.041 0.191 4526 Planarity : 0.005 0.070 5278 Dihedral : 8.856 166.153 4410 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 2.66 % Allowed : 18.56 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.87 (0.15), residues: 3642 helix: 1.92 (0.13), residues: 1626 sheet: -0.66 (0.21), residues: 581 loop : -0.37 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 58 TYR 0.016 0.001 TYR A 50 PHE 0.033 0.001 PHE F 59 TRP 0.014 0.001 TRP F 167 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (29899) covalent geometry : angle 0.60130 / 0.30 (40868) hydrogen bonds : bond 0.03564 / 2.44 ( 1317) hydrogen bonds : angle 4.42878 / 3.23 ( 3726) metal coordination : bond 0.00246 / 0.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 497 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7478 (mtm110) REVERT: A 10 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7729 (p) REVERT: A 71 ARG cc_start: 0.7859 (pmt170) cc_final: 0.7530 (pmt170) REVERT: A 183 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 279 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: A 575 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 6 CYS cc_start: 0.8125 (t) cc_final: 0.7871 (m) REVERT: B 71 ARG cc_start: 0.7632 (pmm-80) cc_final: 0.7304 (pmm-80) REVERT: B 93 GLN cc_start: 0.6142 (pm20) cc_final: 0.5808 (pp30) REVERT: B 96 HIS cc_start: 0.7892 (m170) cc_final: 0.7118 (m170) REVERT: B 106 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7633 (mmtp) REVERT: B 139 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7559 (ptp90) REVERT: B 154 ASN cc_start: 0.8416 (t0) cc_final: 0.8021 (t0) REVERT: B 329 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8050 (ttt90) REVERT: D 2 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7458 (mtm180) REVERT: D 32 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8505 (t) REVERT: D 39 LYS cc_start: 0.8401 (tppt) cc_final: 0.8193 (tptp) REVERT: D 467 ASP cc_start: 0.7908 (t0) cc_final: 0.7590 (p0) REVERT: D 491 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8304 (mtt90) REVERT: D 524 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: F 8 VAL cc_start: 0.8545 (p) cc_final: 0.8328 (m) REVERT: F 19 MET cc_start: 0.8168 (mtp) cc_final: 0.7712 (mtm) REVERT: F 39 LYS cc_start: 0.7901 (tptp) cc_final: 0.7537 (tptp) REVERT: F 71 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7312 (mtm110) REVERT: F 164 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6543 (pp20) REVERT: F 196 MET cc_start: 0.8447 (mtp) cc_final: 0.7932 (mmp) REVERT: F 199 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.8152 (mmm160) REVERT: F 203 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7365 (tm-30) REVERT: F 243 ASP cc_start: 0.8166 (t0) cc_final: 0.7807 (t70) REVERT: F 275 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8018 (mtmt) REVERT: F 528 SER cc_start: 0.8788 (m) cc_final: 0.8335 (p) REVERT: F 529 GLU cc_start: 0.8489 (mp0) cc_final: 0.8245 (mp0) REVERT: E 28 ASP cc_start: 0.7914 (t0) cc_final: 0.7568 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8280 (m-80) cc_final: 0.7878 (m-10) REVERT: E 71 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7774 (mtm-85) REVERT: E 80 GLU cc_start: 0.8060 (tp30) cc_final: 0.7634 (mp0) REVERT: E 130 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7383 (mt-10) REVERT: E 206 LEU cc_start: 0.8699 (mm) cc_final: 0.8399 (mt) REVERT: E 236 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7875 (ttp80) REVERT: E 246 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: E 349 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8589 (mp) REVERT: E 517 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8701 (mtpm) REVERT: C 78 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8213 (pp) REVERT: C 113 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: C 279 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: C 405 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8121 (mtt90) REVERT: C 529 GLU cc_start: 0.8218 (mp0) cc_final: 0.7988 (mp0) outliers start: 79 outliers final: 35 residues processed: 542 average time/residue: 0.8785 time to fit residues: 533.2059 Evaluate side-chains 543 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 495 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 31 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 281 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 25 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS E 546 ASN C 20 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 488 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081512 restraints weight = 57929.085| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.30 r_work: 0.3102 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29917 Z= 0.153 Angle : 0.616 10.372 40868 Z= 0.309 Chirality : 0.041 0.187 4526 Planarity : 0.005 0.090 5278 Dihedral : 8.792 165.456 4410 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 2.76 % Allowed : 19.00 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.84 (0.14), residues: 3642 helix: 1.85 (0.13), residues: 1634 sheet: -0.57 (0.22), residues: 568 loop : -0.39 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 58 TYR 0.017 0.001 TYR A 50 PHE 0.040 0.001 PHE F 59 TRP 0.013 0.001 TRP F 167 HIS 0.008 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (29899) covalent geometry : angle 0.61557 / 0.31 (40868) hydrogen bonds : bond 0.03654 / 2.50 ( 1317) hydrogen bonds : angle 4.41173 / 3.21 ( 3726) metal coordination : bond 0.00234 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 505 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7495 (mtm110) REVERT: A 10 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 71 ARG cc_start: 0.7869 (pmt170) cc_final: 0.7543 (pmt170) REVERT: A 183 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 279 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: A 575 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: B 6 CYS cc_start: 0.8181 (t) cc_final: 0.7932 (m) REVERT: B 71 ARG cc_start: 0.7722 (pmm-80) cc_final: 0.7522 (mpp80) REVERT: B 139 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7581 (ptp90) REVERT: B 154 ASN cc_start: 0.8479 (t0) cc_final: 0.8053 (t0) REVERT: B 329 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8123 (ttt-90) REVERT: D 2 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7462 (mtm180) REVERT: D 32 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8555 (t) REVERT: D 77 MET cc_start: 0.8109 (ptm) cc_final: 0.7893 (ptm) REVERT: D 203 GLU cc_start: 0.8107 (tp30) cc_final: 0.7803 (tm-30) REVERT: D 333 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7983 (mmm-85) REVERT: D 385 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8410 (mtm-85) REVERT: D 467 ASP cc_start: 0.8014 (t0) cc_final: 0.7808 (t0) REVERT: D 491 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8300 (mtt90) REVERT: D 524 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: F 8 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8286 (m) REVERT: F 19 MET cc_start: 0.8100 (mtp) cc_final: 0.7657 (mtm) REVERT: F 22 LEU cc_start: 0.9060 (mt) cc_final: 0.8599 (mp) REVERT: F 39 LYS cc_start: 0.7959 (tptp) cc_final: 0.7597 (tptp) REVERT: F 68 GLU cc_start: 0.7174 (pm20) cc_final: 0.6960 (pm20) REVERT: F 71 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7240 (mtm110) REVERT: F 164 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6489 (pp20) REVERT: F 199 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8145 (mmm160) REVERT: F 203 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7372 (tm-30) REVERT: F 243 ASP cc_start: 0.8194 (t0) cc_final: 0.7828 (t70) REVERT: F 275 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8032 (mtmt) REVERT: F 528 SER cc_start: 0.8784 (m) cc_final: 0.8342 (p) REVERT: F 529 GLU cc_start: 0.8467 (mp0) cc_final: 0.8230 (mp0) REVERT: E 59 PHE cc_start: 0.8277 (m-80) cc_final: 0.7887 (m-10) REVERT: E 71 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7762 (mtm-85) REVERT: E 130 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 206 LEU cc_start: 0.8749 (mm) cc_final: 0.8449 (mt) REVERT: E 236 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7882 (ttp80) REVERT: E 246 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: E 349 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8590 (mp) REVERT: E 517 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8702 (mtpm) REVERT: C 1 MET cc_start: 0.8033 (ppp) cc_final: 0.7719 (tmm) REVERT: C 78 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 80 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: C 196 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: C 279 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: C 405 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8129 (mtt90) REVERT: C 529 GLU cc_start: 0.8227 (mp0) cc_final: 0.7985 (mp0) outliers start: 82 outliers final: 42 residues processed: 556 average time/residue: 0.9220 time to fit residues: 574.1815 Evaluate side-chains 542 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 485 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 176 optimal weight: 3.9990 chunk 220 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 325 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 353 optimal weight: 0.5980 chunk 310 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS B 546 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 136 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 488 HIS E 546 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 525 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082008 restraints weight = 57781.381| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.31 r_work: 0.3113 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29917 Z= 0.137 Angle : 0.639 12.297 40868 Z= 0.321 Chirality : 0.041 0.195 4526 Planarity : 0.005 0.075 5278 Dihedral : 8.735 164.984 4410 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 2.59 % Allowed : 19.84 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.95 (0.14), residues: 3642 helix: 1.98 (0.13), residues: 1617 sheet: -0.56 (0.22), residues: 563 loop : -0.34 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 58 TYR 0.017 0.001 TYR A 50 PHE 0.045 0.001 PHE F 51 TRP 0.012 0.001 TRP F 167 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (29899) covalent geometry : angle 0.63911 / 0.32 (40868) hydrogen bonds : bond 0.03475 / 2.38 ( 1317) hydrogen bonds : angle 4.36162 / 3.17 ( 3726) metal coordination : bond 0.00516 / 0.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 499 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7490 (mtm110) REVERT: A 10 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 71 ARG cc_start: 0.7887 (pmt170) cc_final: 0.7538 (pmt170) REVERT: A 183 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 192 ARG cc_start: 0.8428 (ptp-170) cc_final: 0.7856 (ptp-110) REVERT: A 279 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 575 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: B 6 CYS cc_start: 0.8212 (t) cc_final: 0.7937 (m) REVERT: B 139 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7659 (ptp90) REVERT: B 154 ASN cc_start: 0.8404 (t0) cc_final: 0.8023 (t0) REVERT: B 329 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8135 (ttt-90) REVERT: D 2 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7399 (mtm180) REVERT: D 32 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8490 (t) REVERT: D 77 MET cc_start: 0.8073 (ptm) cc_final: 0.7839 (ptm) REVERT: D 192 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7233 (pmm-80) REVERT: D 333 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8052 (mmm-85) REVERT: D 385 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8483 (mtm-85) REVERT: D 491 ARG cc_start: 0.8586 (mmt90) cc_final: 0.8300 (mtt90) REVERT: D 524 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: F 8 VAL cc_start: 0.8528 (p) cc_final: 0.8293 (m) REVERT: F 10 THR cc_start: 0.8743 (m) cc_final: 0.8454 (p) REVERT: F 19 MET cc_start: 0.8075 (mtp) cc_final: 0.7626 (mtm) REVERT: F 39 LYS cc_start: 0.7958 (tptp) cc_final: 0.7643 (tptp) REVERT: F 68 GLU cc_start: 0.7153 (pm20) cc_final: 0.6951 (pm20) REVERT: F 71 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7207 (mtm110) REVERT: F 164 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6382 (pp20) REVERT: F 196 MET cc_start: 0.8319 (mmp) cc_final: 0.7966 (mmp) REVERT: F 199 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8185 (mmm160) REVERT: F 203 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7409 (tm-30) REVERT: F 243 ASP cc_start: 0.8170 (t0) cc_final: 0.7813 (t70) REVERT: F 275 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8032 (mtmt) REVERT: F 385 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8105 (mtm110) REVERT: F 528 SER cc_start: 0.8788 (m) cc_final: 0.8330 (p) REVERT: F 529 GLU cc_start: 0.8468 (mp0) cc_final: 0.8253 (mp0) REVERT: E 28 ASP cc_start: 0.7919 (t0) cc_final: 0.7544 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8258 (m-80) cc_final: 0.7861 (m-10) REVERT: E 71 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7734 (mtm-85) REVERT: E 80 GLU cc_start: 0.8085 (tp30) cc_final: 0.7631 (mp0) REVERT: E 130 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7386 (mt-10) REVERT: E 133 PHE cc_start: 0.5054 (m-10) cc_final: 0.4842 (m-10) REVERT: E 144 LEU cc_start: 0.8805 (mm) cc_final: 0.8572 (mm) REVERT: E 236 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7860 (ttp80) REVERT: E 246 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: E 517 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8692 (mtpm) REVERT: C 50 TYR cc_start: 0.8702 (t80) cc_final: 0.8463 (t80) REVERT: C 77 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7922 (tpt) REVERT: C 279 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: C 405 ARG cc_start: 0.8386 (tpp80) cc_final: 0.8145 (mtt90) REVERT: C 529 GLU cc_start: 0.8206 (mp0) cc_final: 0.7962 (mp0) outliers start: 77 outliers final: 40 residues processed: 544 average time/residue: 0.9207 time to fit residues: 560.9277 Evaluate side-chains 533 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 483 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 356 optimal weight: 1.9990 chunk 349 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 204 optimal weight: 0.1980 chunk 313 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 20 GLN E 54 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 488 HIS C 525 GLN C 591 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081638 restraints weight = 57705.237| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.29 r_work: 0.3106 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29917 Z= 0.159 Angle : 0.659 12.344 40868 Z= 0.331 Chirality : 0.042 0.190 4526 Planarity : 0.005 0.094 5278 Dihedral : 8.725 164.648 4410 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.19 % Allowed : 20.54 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.14), residues: 3642 helix: 1.90 (0.13), residues: 1622 sheet: -0.54 (0.22), residues: 561 loop : -0.36 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 58 TYR 0.019 0.001 TYR A 50 PHE 0.057 0.002 PHE F 51 TRP 0.012 0.001 TRP F 167 HIS 0.008 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (29899) covalent geometry : angle 0.65860 / 0.33 (40868) hydrogen bonds : bond 0.03619 / 2.48 ( 1317) hydrogen bonds : angle 4.40640 / 3.20 ( 3726) metal coordination : bond 0.00245 / 0.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 490 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7494 (mtm110) REVERT: A 10 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7790 (p) REVERT: A 71 ARG cc_start: 0.7894 (pmt170) cc_final: 0.7550 (pmt170) REVERT: A 183 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8065 (p) REVERT: A 192 ARG cc_start: 0.8457 (ptp-170) cc_final: 0.7880 (ptp-110) REVERT: A 279 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: A 575 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: B 6 CYS cc_start: 0.8179 (t) cc_final: 0.7928 (m) REVERT: B 139 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7907 (ptt-90) REVERT: B 154 ASN cc_start: 0.8420 (t0) cc_final: 0.8051 (t0) REVERT: B 329 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8147 (ttt-90) REVERT: D 2 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: D 32 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8429 (t) REVERT: D 71 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7864 (ptp90) REVERT: D 77 MET cc_start: 0.8077 (ptm) cc_final: 0.7839 (ptm) REVERT: D 383 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: D 385 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8469 (mtm-85) REVERT: D 524 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 8 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8262 (m) REVERT: F 10 THR cc_start: 0.8757 (m) cc_final: 0.8471 (p) REVERT: F 19 MET cc_start: 0.8075 (mtp) cc_final: 0.7683 (mtm) REVERT: F 39 LYS cc_start: 0.7994 (tptp) cc_final: 0.7679 (tptp) REVERT: F 71 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7305 (mtm110) REVERT: F 164 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: F 196 MET cc_start: 0.8327 (mmp) cc_final: 0.8121 (mmp) REVERT: F 199 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.7955 (mmm-85) REVERT: F 203 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7376 (tm-30) REVERT: F 243 ASP cc_start: 0.8193 (t0) cc_final: 0.7834 (t70) REVERT: F 275 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8034 (mtmt) REVERT: F 528 SER cc_start: 0.8832 (m) cc_final: 0.8392 (p) REVERT: E 28 ASP cc_start: 0.7930 (t0) cc_final: 0.7556 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8280 (m-80) cc_final: 0.7928 (m-10) REVERT: E 71 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7756 (mtm-85) REVERT: E 80 GLU cc_start: 0.8112 (tp30) cc_final: 0.7596 (mp0) REVERT: E 130 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7389 (mt-10) REVERT: E 236 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7865 (ttp80) REVERT: E 246 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: E 517 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8681 (mtpm) REVERT: C 77 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7886 (tpt) REVERT: C 279 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: C 405 ARG cc_start: 0.8400 (tpp80) cc_final: 0.8145 (mtt90) REVERT: C 529 GLU cc_start: 0.8218 (mp0) cc_final: 0.7966 (mp0) outliers start: 65 outliers final: 42 residues processed: 526 average time/residue: 1.0127 time to fit residues: 595.2395 Evaluate side-chains 521 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 467 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 168 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 291 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS B 591 GLN D 154 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081521 restraints weight = 57732.961| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.30 r_work: 0.3104 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29917 Z= 0.162 Angle : 0.685 15.496 40868 Z= 0.343 Chirality : 0.042 0.194 4526 Planarity : 0.005 0.079 5278 Dihedral : 8.677 164.549 4410 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.19 % Allowed : 20.75 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.87 (0.14), residues: 3642 helix: 1.85 (0.13), residues: 1623 sheet: -0.53 (0.22), residues: 568 loop : -0.35 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 49 TYR 0.018 0.001 TYR A 50 PHE 0.057 0.002 PHE F 59 TRP 0.012 0.001 TRP A 216 HIS 0.008 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (29899) covalent geometry : angle 0.68550 / 0.34 (40868) hydrogen bonds : bond 0.03661 / 2.50 ( 1317) hydrogen bonds : angle 4.41804 / 3.20 ( 3726) metal coordination : bond 0.00222 / 0.15 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 483 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7490 (mtm110) REVERT: A 10 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 192 ARG cc_start: 0.8443 (ptp-170) cc_final: 0.7864 (ptp-110) REVERT: A 279 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: A 525 GLN cc_start: 0.8152 (pm20) cc_final: 0.7741 (pm20) REVERT: A 575 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: B 6 CYS cc_start: 0.8198 (t) cc_final: 0.7934 (m) REVERT: B 22 LEU cc_start: 0.8523 (mt) cc_final: 0.8289 (pp) REVERT: B 71 ARG cc_start: 0.7508 (mpp80) cc_final: 0.7222 (mpp80) REVERT: B 154 ASN cc_start: 0.8436 (t0) cc_final: 0.8081 (t0) REVERT: B 329 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8134 (ttt-90) REVERT: D 2 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7385 (mtm180) REVERT: D 22 LEU cc_start: 0.8765 (mt) cc_final: 0.8531 (mm) REVERT: D 32 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8411 (t) REVERT: D 71 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7767 (ptp90) REVERT: D 77 MET cc_start: 0.8089 (ptm) cc_final: 0.7843 (ptm) REVERT: D 154 ASN cc_start: 0.8738 (m-40) cc_final: 0.8488 (m-40) REVERT: D 192 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7246 (pmm-80) REVERT: D 383 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: D 385 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8466 (mtm-85) REVERT: D 524 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: F 8 VAL cc_start: 0.8551 (p) cc_final: 0.8278 (m) REVERT: F 10 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8476 (p) REVERT: F 19 MET cc_start: 0.8011 (mtp) cc_final: 0.7576 (mtm) REVERT: F 22 LEU cc_start: 0.8810 (mm) cc_final: 0.8607 (mp) REVERT: F 71 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7303 (mtm110) REVERT: F 164 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: F 199 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8213 (mmm160) REVERT: F 203 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7403 (tm-30) REVERT: F 243 ASP cc_start: 0.8176 (t0) cc_final: 0.7809 (t70) REVERT: F 275 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8021 (mtmt) REVERT: F 528 SER cc_start: 0.8895 (m) cc_final: 0.8628 (p) REVERT: E 28 ASP cc_start: 0.7923 (t0) cc_final: 0.7544 (OUTLIER) REVERT: E 51 PHE cc_start: 0.8851 (m-10) cc_final: 0.8222 (m-10) REVERT: E 59 PHE cc_start: 0.8246 (m-80) cc_final: 0.7902 (m-80) REVERT: E 71 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7759 (mtm-85) REVERT: E 80 GLU cc_start: 0.8098 (tp30) cc_final: 0.7561 (mp0) REVERT: E 130 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7413 (mt-10) REVERT: E 133 PHE cc_start: 0.5193 (m-10) cc_final: 0.4960 (m-10) REVERT: E 206 LEU cc_start: 0.8709 (mm) cc_final: 0.8406 (mt) REVERT: E 236 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7893 (ttp80) REVERT: E 246 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: E 501 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8097 (mt-10) REVERT: E 517 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8683 (mtpm) REVERT: C 101 LEU cc_start: 0.9038 (pp) cc_final: 0.8826 (pp) REVERT: C 279 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: C 405 ARG cc_start: 0.8400 (tpp80) cc_final: 0.8153 (mtt90) REVERT: C 529 GLU cc_start: 0.8232 (mp0) cc_final: 0.7981 (mp0) outliers start: 65 outliers final: 46 residues processed: 519 average time/residue: 0.9819 time to fit residues: 571.3622 Evaluate side-chains 530 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 474 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 376 GLN Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 63 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 214 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 136 GLN E 54 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS E 546 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082208 restraints weight = 57823.762| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.31 r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29917 Z= 0.143 Angle : 0.687 15.565 40868 Z= 0.345 Chirality : 0.042 0.205 4526 Planarity : 0.006 0.104 5278 Dihedral : 8.577 166.566 4410 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 21.25 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.14), residues: 3642 helix: 1.87 (0.13), residues: 1621 sheet: -0.54 (0.22), residues: 572 loop : -0.33 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 58 TYR 0.018 0.001 TYR A 50 PHE 0.058 0.002 PHE B 59 TRP 0.015 0.001 TRP A 86 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (29899) covalent geometry : angle 0.68684 / 0.34 (40868) hydrogen bonds : bond 0.03524 / 2.40 ( 1317) hydrogen bonds : angle 4.39153 / 3.19 ( 3726) metal coordination : bond 0.00152 / 0.10 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12743.62 seconds wall clock time: 217 minutes 9.43 seconds (13029.43 seconds total)