Starting phenix.real_space_refine on Sat Jun 6 15:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1i_65544/06_2026/9w1i_65544_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1i_65544/06_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_65544/06_2026/9w1i_65544_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1i_65544/06_2026/9w1i_65544_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1i_65544/06_2026/9w1i_65544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1i_65544/06_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-6079/lib/python3.9/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: 6.33, per 1000 atoms: 0.22 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: 2.51 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: 1.18 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: 5.95 Time building geometry restraints manager: 3.30 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=" 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 angle pdb=" N ASN A 316 " pdb=" CA ASN A 316 " pdb=" C ASN A 316 " ideal model delta sigma weight residual 113.50 108.04 5.46 1.23e+00 6.61e-01 1.97e+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: 5.090 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: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.970 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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= 0.214 Angle : 0.562 12.312 40868 Z= 0.304 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 / 0.20 (29899) covalent geometry : angle 0.56213 / 0.30 (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 : 0.908 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: 0.8745 time to fit residues: 686.2989 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 : 1.147 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 89 GLN A 136 GLN A 169 GLN A 473 GLN A 488 HIS A 515 GLN A 546 ASN ** 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 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 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 154 ASN C 390 ASN C 546 ASN C 549 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083390 restraints weight = 56830.535| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3138 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29917 Z= 0.146 Angle : 0.613 12.087 40868 Z= 0.306 Chirality : 0.042 0.193 4526 Planarity : 0.005 0.075 5278 Dihedral : 9.416 169.969 4425 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.79 % Favored : 96.07 % Rotamer: Outliers : 2.93 % Allowed : 13.48 % Favored : 83.59 % 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: 1.07 (0.15), residues: 3642 helix: 2.10 (0.13), residues: 1621 sheet: -0.62 (0.23), residues: 574 loop : -0.26 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 71 TYR 0.012 0.001 TYR F 50 PHE 0.026 0.001 PHE E 59 TRP 0.016 0.001 TRP D 167 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (29899) covalent geometry : angle 0.61325 / 0.31 (40868) hydrogen bonds : bond 0.04063 / 2.78 ( 1317) hydrogen bonds : angle 4.76748 / 3.46 ( 3726) metal coordination : bond 0.00436 / 0.31 ( 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 638 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 551 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7395 (mtm110) REVERT: A 10 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 22 LEU cc_start: 0.8596 (mp) cc_final: 0.8272 (mp) REVERT: A 29 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7689 (mp0) REVERT: A 71 ARG cc_start: 0.7705 (pmt170) cc_final: 0.7491 (pmt170) REVERT: A 183 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8130 (p) REVERT: A 189 HIS cc_start: 0.8081 (m-70) cc_final: 0.7876 (m170) REVERT: A 279 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: B 22 LEU cc_start: 0.8578 (mt) cc_final: 0.8304 (mp) REVERT: B 71 ARG cc_start: 0.7592 (pmm-80) cc_final: 0.7312 (pmm-80) REVERT: B 93 GLN cc_start: 0.6103 (pm20) cc_final: 0.5833 (pp30) REVERT: B 96 HIS cc_start: 0.7921 (m170) cc_final: 0.7564 (m90) REVERT: B 144 LEU cc_start: 0.8184 (tm) cc_final: 0.7965 (tp) REVERT: B 154 ASN cc_start: 0.8605 (t0) cc_final: 0.8196 (t0) REVERT: B 210 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8544 (mtm-85) REVERT: B 329 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8051 (ttt90) REVERT: B 449 GLU cc_start: 0.8156 (tt0) cc_final: 0.7945 (tm-30) REVERT: B 533 LEU cc_start: 0.8302 (tp) cc_final: 0.7980 (tt) REVERT: D 22 LEU cc_start: 0.8578 (mt) cc_final: 0.7789 (mm) REVERT: D 154 ASN cc_start: 0.8581 (m110) cc_final: 0.8376 (t0) REVERT: D 303 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8405 (mp0) REVERT: D 528 SER cc_start: 0.8940 (t) cc_final: 0.8664 (t) REVERT: D 529 GLU cc_start: 0.8194 (mp0) cc_final: 0.7966 (mp0) REVERT: F 8 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8171 (m) REVERT: F 25 GLN cc_start: 0.8145 (tp40) cc_final: 0.7830 (tp-100) REVERT: F 39 LYS cc_start: 0.7813 (tptp) cc_final: 0.7536 (tptp) REVERT: F 71 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7140 (mtm110) REVERT: F 203 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7298 (tm-30) REVERT: F 240 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: F 243 ASP cc_start: 0.8027 (t0) cc_final: 0.7734 (t70) REVERT: F 275 LYS cc_start: 0.8336 (ttmm) cc_final: 0.7972 (mtmt) REVERT: F 526 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7288 (tm-30) REVERT: F 528 SER cc_start: 0.8801 (m) cc_final: 0.8516 (p) REVERT: E 59 PHE cc_start: 0.8268 (m-80) cc_final: 0.7773 (m-80) REVERT: E 130 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7257 (mt-10) REVERT: E 185 GLN cc_start: 0.7836 (mp10) cc_final: 0.7633 (mp10) REVERT: E 206 LEU cc_start: 0.8661 (mm) cc_final: 0.8333 (mt) REVERT: E 517 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8671 (mtpm) REVERT: E 591 GLN cc_start: 0.8275 (mt0) cc_final: 0.8053 (mp10) REVERT: C 96 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7338 (p90) REVERT: C 139 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7394 (ptp90) REVERT: C 405 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8062 (mtt90) outliers start: 87 outliers final: 27 residues processed: 598 average time/residue: 0.9874 time to fit residues: 658.5224 Evaluate side-chains 532 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 498 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 B residue 38 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 210 ARG 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 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 D residue 383 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 E residue 307 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 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: 0.9990 chunk 253 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN A 546 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 269 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** 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 = 0.3461 r_free = 0.3461 target = 0.094288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082369 restraints weight = 56707.519| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.26 r_work: 0.3121 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29917 Z= 0.157 Angle : 0.594 8.842 40868 Z= 0.296 Chirality : 0.042 0.188 4526 Planarity : 0.005 0.074 5278 Dihedral : 9.115 167.925 4417 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.96 % Allowed : 15.03 % Favored : 82.01 % 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: 0.99 (0.15), residues: 3642 helix: 2.01 (0.13), residues: 1626 sheet: -0.64 (0.22), residues: 582 loop : -0.28 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 157 TYR 0.011 0.001 TYR A 50 PHE 0.022 0.001 PHE D 59 TRP 0.013 0.001 TRP B 167 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (29899) covalent geometry : angle 0.59386 / 0.30 (40868) hydrogen bonds : bond 0.03880 / 2.64 ( 1317) hydrogen bonds : angle 4.58383 / 3.33 ( 3726) metal coordination : bond 0.00238 / 0.17 ( 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 603 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 515 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7767 (mtm110) cc_final: 0.6618 (mtm110) REVERT: A 10 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 71 ARG cc_start: 0.7741 (pmt170) cc_final: 0.7458 (pmt170) REVERT: A 183 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 184 LEU cc_start: 0.7877 (tp) cc_final: 0.7642 (tm) REVERT: A 192 ARG cc_start: 0.8470 (ptp-170) cc_final: 0.7879 (ptp-110) REVERT: A 279 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: A 575 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: B 22 LEU cc_start: 0.8460 (mt) cc_final: 0.8116 (mt) REVERT: B 71 ARG cc_start: 0.7625 (pmm-80) cc_final: 0.7290 (pmm-80) REVERT: B 93 GLN cc_start: 0.6117 (pm20) cc_final: 0.5683 (pp30) REVERT: B 96 HIS cc_start: 0.7907 (m170) cc_final: 0.7071 (m90) REVERT: B 144 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7911 (tp) REVERT: B 154 ASN cc_start: 0.8585 (t0) cc_final: 0.8093 (t0) REVERT: B 329 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8036 (ttt90) REVERT: B 533 LEU cc_start: 0.8301 (tp) cc_final: 0.8007 (tt) REVERT: D 77 MET cc_start: 0.8101 (mtp) cc_final: 0.7641 (ttp) REVERT: D 303 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8410 (mp0) REVERT: D 385 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8510 (mtm-85) REVERT: D 440 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8355 (mtt180) REVERT: D 524 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: D 528 SER cc_start: 0.8959 (t) cc_final: 0.8682 (t) REVERT: D 529 GLU cc_start: 0.8222 (mp0) cc_final: 0.7951 (mp0) REVERT: F 8 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (m) REVERT: F 19 MET cc_start: 0.8193 (mtp) cc_final: 0.7767 (mtt) REVERT: F 22 LEU cc_start: 0.9050 (mt) cc_final: 0.8542 (mp) REVERT: F 39 LYS cc_start: 0.7874 (tptp) cc_final: 0.7564 (tptp) REVERT: F 59 PHE cc_start: 0.7509 (m-80) cc_final: 0.7280 (m-80) REVERT: F 71 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7279 (mtm110) REVERT: F 77 MET cc_start: 0.8713 (ttm) cc_final: 0.8233 (mtp) REVERT: F 164 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: F 196 MET cc_start: 0.8598 (mtp) cc_final: 0.8396 (mtp) REVERT: F 199 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.8030 (mtp-110) REVERT: F 203 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7336 (tm-30) REVERT: F 240 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: F 243 ASP cc_start: 0.8116 (t0) cc_final: 0.7780 (t70) REVERT: F 275 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8006 (mtmt) REVERT: F 385 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7761 (mtm180) REVERT: F 526 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7274 (tm-30) REVERT: F 528 SER cc_start: 0.8855 (m) cc_final: 0.8576 (p) REVERT: E 59 PHE cc_start: 0.8386 (m-80) cc_final: 0.8044 (m-10) REVERT: E 130 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7332 (mt-10) REVERT: E 133 PHE cc_start: 0.4719 (m-10) cc_final: 0.4435 (m-10) REVERT: E 236 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7852 (ttp80) REVERT: E 348 GLU cc_start: 0.8630 (tt0) cc_final: 0.8041 (tt0) REVERT: E 405 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8390 (mtt-85) REVERT: E 517 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8746 (mtpt) REVERT: E 591 GLN cc_start: 0.8302 (mt0) cc_final: 0.8061 (mp10) REVERT: C 29 GLU cc_start: 0.8146 (tt0) cc_final: 0.7907 (tt0) REVERT: C 77 MET cc_start: 0.8513 (mmt) cc_final: 0.8129 (mmm) REVERT: C 96 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7514 (p90) REVERT: C 196 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: C 279 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: C 302 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8562 (mp0) REVERT: C 405 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8112 (mtt90) REVERT: C 528 SER cc_start: 0.8880 (m) cc_final: 0.8674 (t) outliers start: 88 outliers final: 30 residues processed: 571 average time/residue: 1.0000 time to fit residues: 638.5024 Evaluate side-chains 539 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 497 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 54 HIS 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 144 LEU 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 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 268 THR Chi-restraints excluded: chain D residue 271 GLU 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 240 GLU 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 307 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 154 ASN 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 398 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: 1.9990 chunk 104 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 271 optimal weight: 0.0050 chunk 305 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 546 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 591 GLN F 169 GLN E 488 HIS ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 513 ASN C 525 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082727 restraints weight = 56496.833| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.26 r_work: 0.3127 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29917 Z= 0.140 Angle : 0.579 8.946 40868 Z= 0.289 Chirality : 0.041 0.185 4526 Planarity : 0.005 0.075 5278 Dihedral : 8.874 166.535 4412 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.99 % Allowed : 15.70 % Favored : 81.30 % 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: 1.02 (0.15), residues: 3642 helix: 2.04 (0.13), residues: 1625 sheet: -0.63 (0.22), residues: 586 loop : -0.26 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 192 TYR 0.012 0.001 TYR A 50 PHE 0.014 0.001 PHE E 133 TRP 0.012 0.001 TRP E 190 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (29899) covalent geometry : angle 0.57914 / 0.29 (40868) hydrogen bonds : bond 0.03609 / 2.46 ( 1317) hydrogen bonds : angle 4.45412 / 3.24 ( 3726) metal coordination : bond 0.00215 / 0.14 ( 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 594 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 505 time to evaluate : 1.260 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: 0.7778 (mtm110) cc_final: 0.7472 (mtm110) REVERT: A 10 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 71 ARG cc_start: 0.7785 (pmt170) cc_final: 0.7462 (pmt170) REVERT: A 183 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 279 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: A 575 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 71 ARG cc_start: 0.7569 (pmm-80) cc_final: 0.7234 (pmm-80) REVERT: B 93 GLN cc_start: 0.6163 (pm20) cc_final: 0.5773 (pp30) REVERT: B 96 HIS cc_start: 0.7900 (m170) cc_final: 0.7087 (m90) REVERT: B 139 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7587 (ptp90) REVERT: B 154 ASN cc_start: 0.8479 (t0) cc_final: 0.8034 (t0) REVERT: B 157 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6657 (mpp80) REVERT: B 329 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8032 (ttt90) REVERT: B 529 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: B 533 LEU cc_start: 0.8270 (tp) cc_final: 0.8006 (tt) REVERT: D 39 LYS cc_start: 0.8466 (tppt) cc_final: 0.8222 (tptp) REVERT: D 77 MET cc_start: 0.8126 (mtp) cc_final: 0.7827 (ttm) REVERT: D 303 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8367 (mp0) REVERT: D 385 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8464 (mtm-85) REVERT: D 467 ASP cc_start: 0.7924 (t0) cc_final: 0.7709 (p0) REVERT: D 524 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: D 528 SER cc_start: 0.8960 (t) cc_final: 0.8741 (t) REVERT: D 529 GLU cc_start: 0.8231 (mp0) cc_final: 0.8029 (mp0) REVERT: F 8 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (m) REVERT: F 27 PHE cc_start: 0.8406 (m-80) cc_final: 0.8007 (m-80) REVERT: F 39 LYS cc_start: 0.7871 (tptp) cc_final: 0.7514 (tptp) REVERT: F 71 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7211 (mtm110) REVERT: F 77 MET cc_start: 0.8700 (ttm) cc_final: 0.8294 (mtp) REVERT: F 112 MET cc_start: 0.8631 (mmm) cc_final: 0.8392 (mmm) REVERT: F 164 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6531 (pp20) REVERT: F 196 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8392 (mtp) REVERT: F 203 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7381 (tm-30) REVERT: F 240 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: F 243 ASP cc_start: 0.8118 (t0) cc_final: 0.7779 (t70) REVERT: F 275 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8016 (mtmt) REVERT: F 526 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7268 (tm-30) REVERT: F 528 SER cc_start: 0.8897 (m) cc_final: 0.8556 (p) REVERT: E 28 ASP cc_start: 0.7871 (t0) cc_final: 0.7519 (t0) REVERT: E 59 PHE cc_start: 0.8388 (m-80) cc_final: 0.8009 (m-80) REVERT: E 130 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7329 (mt-10) REVERT: E 132 ARG cc_start: 0.8106 (ptt90) cc_final: 0.7838 (ppt170) REVERT: E 133 PHE cc_start: 0.4843 (m-80) cc_final: 0.4551 (m-10) REVERT: E 236 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7852 (ttp80) REVERT: E 246 GLN cc_start: 0.8560 (mt0) cc_final: 0.8342 (mp10) REVERT: E 517 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8748 (mtpt) REVERT: E 591 GLN cc_start: 0.8290 (mt0) cc_final: 0.8065 (mp10) REVERT: C 21 LEU cc_start: 0.8950 (tm) cc_final: 0.8714 (tp) REVERT: C 29 GLU cc_start: 0.8112 (tt0) cc_final: 0.7835 (mm-30) REVERT: C 58 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7552 (ttm110) REVERT: C 77 MET cc_start: 0.8479 (mmt) cc_final: 0.8068 (mmm) REVERT: C 106 LYS cc_start: 0.8034 (mttm) cc_final: 0.7800 (mttm) REVERT: C 113 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: C 136 GLN cc_start: 0.7552 (mp10) cc_final: 0.7267 (pm20) REVERT: C 139 ARG cc_start: 0.7268 (mpp80) cc_final: 0.6764 (mpp80) REVERT: C 196 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7047 (mpp) REVERT: C 279 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: C 405 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8105 (mtt90) REVERT: C 528 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8387 (p) outliers start: 89 outliers final: 36 residues processed: 560 average time/residue: 0.9958 time to fit residues: 620.9156 Evaluate side-chains 536 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 486 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 78 LEU 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 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 D residue 6 CYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 53 MET 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 8 VAL 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 196 MET Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 54 HIS Chi-restraints excluded: chain E residue 99 ILE 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 E residue 491 ARG Chi-restraints excluded: chain C residue 54 HIS 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 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 398 GLU Chi-restraints excluded: chain C residue 528 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: 0.0970 chunk 155 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 342 optimal weight: 1.9990 chunk 138 optimal weight: 0.0050 chunk 175 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS B 269 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 25 GLN F 169 GLN E 185 GLN E 488 HIS E 546 ASN C 20 GLN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 525 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082809 restraints weight = 56537.262| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.29 r_work: 0.3131 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29917 Z= 0.129 Angle : 0.576 9.533 40868 Z= 0.288 Chirality : 0.040 0.182 4526 Planarity : 0.005 0.072 5278 Dihedral : 8.700 165.470 4410 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 2.72 % Allowed : 16.91 % Favored : 80.36 % 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: 1.06 (0.15), residues: 3642 helix: 2.08 (0.13), residues: 1622 sheet: -0.57 (0.22), residues: 586 loop : -0.26 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 49 TYR 0.015 0.001 TYR A 50 PHE 0.034 0.001 PHE F 59 TRP 0.035 0.001 TRP E 12 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (29899) covalent geometry : angle 0.57622 / 0.29 (40868) hydrogen bonds : bond 0.03441 / 2.34 ( 1317) hydrogen bonds : angle 4.35128 / 3.17 ( 3726) metal coordination : bond 0.00255 / 0.19 ( 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 585 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 504 time to evaluate : 1.146 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: 0.7774 (mtm110) cc_final: 0.7454 (mtm110) REVERT: A 10 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7797 (p) REVERT: A 71 ARG cc_start: 0.7834 (pmt170) cc_final: 0.7503 (pmt170) REVERT: A 192 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.7874 (ptp-110) REVERT: A 279 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: A 575 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 6 CYS cc_start: 0.8085 (t) cc_final: 0.7835 (m) REVERT: B 41 SER cc_start: 0.7943 (OUTLIER) cc_final: 0.7615 (p) REVERT: B 71 ARG cc_start: 0.7584 (pmm-80) cc_final: 0.7231 (pmm-80) REVERT: B 139 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7641 (ptp90) REVERT: B 154 ASN cc_start: 0.8415 (t0) cc_final: 0.7994 (t0) REVERT: B 329 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8035 (ttt90) REVERT: B 449 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: B 533 LEU cc_start: 0.8247 (tp) cc_final: 0.8025 (tt) REVERT: D 32 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8539 (t) REVERT: D 39 LYS cc_start: 0.8453 (tppt) cc_final: 0.8189 (tptp) REVERT: D 385 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8477 (mtm-85) REVERT: D 467 ASP cc_start: 0.8008 (t0) cc_final: 0.7766 (t0) REVERT: D 491 ARG cc_start: 0.8622 (mmt90) cc_final: 0.8329 (mtt90) REVERT: D 524 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: D 529 GLU cc_start: 0.8279 (mp0) cc_final: 0.7981 (pm20) REVERT: F 8 VAL cc_start: 0.8481 (p) cc_final: 0.8252 (m) REVERT: F 19 MET cc_start: 0.8064 (mtp) cc_final: 0.7629 (mtm) REVERT: F 22 LEU cc_start: 0.8977 (mp) cc_final: 0.8751 (mm) REVERT: F 39 LYS cc_start: 0.7889 (tptp) cc_final: 0.7520 (tptp) REVERT: F 68 GLU cc_start: 0.7037 (pm20) cc_final: 0.6752 (pm20) REVERT: F 71 ARG cc_start: 0.7471 (mtm110) cc_final: 0.7095 (mtm110) REVERT: F 77 MET cc_start: 0.8689 (ttm) cc_final: 0.8372 (mtm) REVERT: F 164 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6453 (pp20) REVERT: F 203 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7363 (tm-30) REVERT: F 240 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: F 243 ASP cc_start: 0.8114 (t0) cc_final: 0.7768 (t70) REVERT: F 275 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8052 (mtmt) REVERT: F 385 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.8024 (mtm-85) REVERT: F 526 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7219 (tm-30) REVERT: F 528 SER cc_start: 0.8881 (m) cc_final: 0.8603 (p) REVERT: E 28 ASP cc_start: 0.7908 (t0) cc_final: 0.7526 (t0) REVERT: E 53 MET cc_start: 0.7508 (tmm) cc_final: 0.7283 (tmm) REVERT: E 59 PHE cc_start: 0.8376 (m-80) cc_final: 0.8031 (m-10) REVERT: E 130 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7448 (mt-10) REVERT: E 132 ARG cc_start: 0.8100 (ptt90) cc_final: 0.7898 (ppt170) REVERT: E 133 PHE cc_start: 0.4739 (m-80) cc_final: 0.4471 (m-10) REVERT: E 236 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7866 (ttp80) REVERT: E 246 GLN cc_start: 0.8539 (mt0) cc_final: 0.8334 (mt0) REVERT: E 517 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8739 (mtpt) REVERT: E 591 GLN cc_start: 0.8287 (mt0) cc_final: 0.8063 (mp10) REVERT: C 21 LEU cc_start: 0.8942 (tm) cc_final: 0.8711 (tp) REVERT: C 29 GLU cc_start: 0.8173 (tt0) cc_final: 0.7850 (mm-30) REVERT: C 50 TYR cc_start: 0.8709 (t80) cc_final: 0.8495 (t80) REVERT: C 58 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7494 (ttm110) REVERT: C 77 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: C 196 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7153 (mpp) REVERT: C 279 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: C 398 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: C 405 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8113 (mtt90) REVERT: C 517 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8752 (mmmm) outliers start: 81 outliers final: 29 residues processed: 549 average time/residue: 0.9847 time to fit residues: 603.1478 Evaluate side-chains 516 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 474 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 54 HIS 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 38 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 449 GLU 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 240 GLU 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 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 77 MET Chi-restraints excluded: chain C residue 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 398 GLU 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: 0.0670 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 349 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN ** 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 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 20 GLN F 169 GLN E 76 HIS ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 488 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082764 restraints weight = 56585.825| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.26 r_work: 0.3132 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2607 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= 0.142 Angle : 0.594 10.413 40868 Z= 0.299 Chirality : 0.041 0.183 4526 Planarity : 0.005 0.076 5278 Dihedral : 8.619 164.948 4410 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 2.86 % Allowed : 17.75 % Favored : 79.39 % 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: 1.06 (0.15), residues: 3642 helix: 2.05 (0.13), residues: 1622 sheet: -0.54 (0.22), residues: 586 loop : -0.25 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 58 TYR 0.015 0.001 TYR A 50 PHE 0.034 0.001 PHE F 59 TRP 0.031 0.001 TRP E 12 HIS 0.008 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (29899) covalent geometry : angle 0.59363 / 0.30 (40868) hydrogen bonds : bond 0.03473 / 2.38 ( 1317) hydrogen bonds : angle 4.30535 / 3.13 ( 3726) metal coordination : bond 0.00200 / 0.14 ( 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 577 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 492 time to evaluate : 1.258 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: 0.7771 (mtm110) cc_final: 0.7460 (mtm110) REVERT: A 10 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 70 LEU cc_start: 0.8527 (tp) cc_final: 0.8186 (tp) REVERT: A 71 ARG cc_start: 0.7854 (pmt170) cc_final: 0.7514 (pmt170) REVERT: A 86 TRP cc_start: 0.8805 (t60) cc_final: 0.8495 (t60) REVERT: A 192 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.7863 (ptp-110) REVERT: A 279 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: A 575 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: B 6 CYS cc_start: 0.8147 (t) cc_final: 0.7902 (m) REVERT: B 71 ARG cc_start: 0.7650 (pmm-80) cc_final: 0.7429 (pmm-80) REVERT: B 154 ASN cc_start: 0.8407 (t0) cc_final: 0.8044 (t0) REVERT: B 157 ARG cc_start: 0.6926 (mtm-85) cc_final: 0.6693 (mpp80) REVERT: B 329 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8059 (ttt-90) REVERT: B 449 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: B 533 LEU cc_start: 0.8251 (tp) cc_final: 0.8026 (tt) REVERT: D 32 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8560 (t) REVERT: D 71 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7865 (ptp-110) REVERT: D 77 MET cc_start: 0.8044 (ptm) cc_final: 0.7775 (ptm) REVERT: D 385 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8503 (mtm-85) REVERT: D 491 ARG cc_start: 0.8604 (mmt90) cc_final: 0.8299 (mtt90) REVERT: D 524 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: D 529 GLU cc_start: 0.8209 (mp0) cc_final: 0.7963 (pm20) REVERT: F 2 ARG cc_start: 0.7850 (mpp-170) cc_final: 0.7447 (mtm180) REVERT: F 8 VAL cc_start: 0.8534 (p) cc_final: 0.8310 (m) REVERT: F 10 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8455 (p) REVERT: F 19 MET cc_start: 0.7989 (mtp) cc_final: 0.7577 (mtm) REVERT: F 27 PHE cc_start: 0.8346 (m-80) cc_final: 0.7970 (m-80) REVERT: F 39 LYS cc_start: 0.7939 (tptp) cc_final: 0.7626 (tptp) REVERT: F 68 GLU cc_start: 0.7100 (pm20) cc_final: 0.6888 (pm20) REVERT: F 71 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7114 (mtm110) REVERT: F 77 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: F 112 MET cc_start: 0.8573 (mmm) cc_final: 0.8353 (mmm) REVERT: F 164 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6414 (pp20) REVERT: F 203 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7341 (tm-30) REVERT: F 240 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: F 243 ASP cc_start: 0.8116 (t0) cc_final: 0.7787 (t70) REVERT: F 275 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8067 (mtmt) REVERT: F 385 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7761 (mtm180) REVERT: F 526 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7222 (tm-30) REVERT: F 528 SER cc_start: 0.8930 (m) cc_final: 0.8682 (p) REVERT: E 28 ASP cc_start: 0.7905 (t0) cc_final: 0.7547 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8366 (m-80) cc_final: 0.7967 (m-10) REVERT: E 71 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7243 (mtt90) REVERT: E 130 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7422 (mt-10) REVERT: E 133 PHE cc_start: 0.4760 (m-80) cc_final: 0.4465 (m-10) REVERT: E 203 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: E 236 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7857 (ttp80) REVERT: E 246 GLN cc_start: 0.8537 (mt0) cc_final: 0.8309 (mt0) REVERT: E 349 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (mp) REVERT: E 517 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8696 (mtpm) REVERT: E 591 GLN cc_start: 0.8318 (mt0) cc_final: 0.8079 (mp10) REVERT: C 21 LEU cc_start: 0.8946 (tm) cc_final: 0.8726 (tp) REVERT: C 29 GLU cc_start: 0.8117 (tt0) cc_final: 0.7816 (mm-30) REVERT: C 58 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7500 (ttm110) REVERT: C 139 ARG cc_start: 0.7317 (mpp80) cc_final: 0.6915 (mtm-85) REVERT: C 196 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7103 (mpp) REVERT: C 279 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: C 308 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 398 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: C 405 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8112 (mtt90) REVERT: C 528 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8318 (p) outliers start: 85 outliers final: 37 residues processed: 540 average time/residue: 0.9887 time to fit residues: 595.8067 Evaluate side-chains 537 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 248 LYS 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 172 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 459 THR 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 524 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 77 MET 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 240 GLU 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 203 GLU 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 459 THR Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 528 SER 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: 0.7980 chunk 181 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 323 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN A 488 HIS A 546 ASN ** 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 113 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 169 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS E 546 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082056 restraints weight = 56870.471| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.27 r_work: 0.3122 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29917 Z= 0.160 Angle : 0.614 10.609 40868 Z= 0.307 Chirality : 0.041 0.184 4526 Planarity : 0.005 0.081 5278 Dihedral : 8.607 164.781 4410 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 2.89 % Allowed : 18.36 % Favored : 78.75 % 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: 1.95 (0.13), residues: 1628 sheet: -0.56 (0.22), residues: 586 loop : -0.26 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 160 TYR 0.015 0.001 TYR A 50 PHE 0.038 0.001 PHE F 59 TRP 0.027 0.001 TRP E 12 HIS 0.008 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (29899) covalent geometry : angle 0.61402 / 0.31 (40868) hydrogen bonds : bond 0.03596 / 2.46 ( 1317) hydrogen bonds : angle 4.32064 / 3.14 ( 3726) metal coordination : bond 0.00232 / 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 581 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 495 time to evaluate : 1.192 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: 0.7832 (mtm110) cc_final: 0.7531 (mtm110) REVERT: A 10 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 70 LEU cc_start: 0.8536 (tp) cc_final: 0.8227 (tp) REVERT: A 71 ARG cc_start: 0.7899 (pmt170) cc_final: 0.7553 (pmt170) REVERT: A 192 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.7874 (ptp-110) REVERT: A 279 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: A 575 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: B 6 CYS cc_start: 0.8202 (t) cc_final: 0.7942 (m) REVERT: B 154 ASN cc_start: 0.8484 (t0) cc_final: 0.8068 (t0) REVERT: B 329 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8098 (ttt-90) REVERT: B 430 ASP cc_start: 0.8480 (t0) cc_final: 0.8234 (t0) REVERT: B 449 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: B 533 LEU cc_start: 0.8288 (tp) cc_final: 0.8053 (tt) REVERT: D 32 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8502 (t) REVERT: D 77 MET cc_start: 0.8108 (ptm) cc_final: 0.7866 (ptm) REVERT: D 383 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: D 385 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8485 (mtm-85) REVERT: D 524 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: F 2 ARG cc_start: 0.7839 (mpp-170) cc_final: 0.7403 (mtm180) REVERT: F 8 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8284 (m) REVERT: F 10 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8482 (p) REVERT: F 19 MET cc_start: 0.8033 (mtp) cc_final: 0.7583 (mtm) REVERT: F 71 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7199 (mtm110) REVERT: F 164 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6440 (pp20) REVERT: F 203 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7373 (tm-30) REVERT: F 240 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: F 243 ASP cc_start: 0.8137 (t0) cc_final: 0.7790 (t70) REVERT: F 275 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8080 (mtmt) REVERT: F 385 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7753 (mtm180) REVERT: F 526 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7246 (tm-30) REVERT: F 528 SER cc_start: 0.8898 (m) cc_final: 0.8671 (p) REVERT: E 28 ASP cc_start: 0.7947 (t0) cc_final: 0.7586 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8335 (m-80) cc_final: 0.7940 (m-10) REVERT: E 71 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7273 (mtt90) REVERT: E 80 GLU cc_start: 0.8007 (tp30) cc_final: 0.7552 (mp0) REVERT: E 130 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7388 (mt-10) REVERT: E 133 PHE cc_start: 0.4798 (m-80) cc_final: 0.4471 (m-10) REVERT: E 203 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: E 236 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7879 (ttp80) REVERT: E 517 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8701 (mtpm) REVERT: C 101 LEU cc_start: 0.9042 (pp) cc_final: 0.8817 (pp) REVERT: C 196 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: C 279 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: C 308 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7984 (mm-30) REVERT: C 398 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: C 405 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8135 (mtt90) REVERT: C 528 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8318 (p) outliers start: 86 outliers final: 45 residues processed: 543 average time/residue: 0.9744 time to fit residues: 590.6896 Evaluate side-chains 533 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 473 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 47 LEU 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 248 LYS 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 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 459 THR 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 383 GLU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 THR 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 240 GLU 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 54 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 203 GLU 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 35 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 528 SER 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: 0.9980 chunk 59 optimal weight: 0.9990 chunk 325 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 320 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN ** 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** B 591 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 20 GLN F 136 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082008 restraints weight = 56883.514| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.27 r_work: 0.3116 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2737 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= 0.160 Angle : 0.638 12.038 40868 Z= 0.321 Chirality : 0.042 0.194 4526 Planarity : 0.005 0.083 5278 Dihedral : 8.621 166.911 4410 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.69 % Allowed : 18.96 % Favored : 78.35 % 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: 0.97 (0.14), residues: 3642 helix: 1.92 (0.13), residues: 1629 sheet: -0.50 (0.22), residues: 568 loop : -0.28 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 58 TYR 0.021 0.001 TYR A 50 PHE 0.049 0.001 PHE F 59 TRP 0.030 0.001 TRP E 12 HIS 0.008 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (29899) covalent geometry : angle 0.63843 / 0.32 (40868) hydrogen bonds : bond 0.03576 / 2.45 ( 1317) hydrogen bonds : angle 4.31913 / 3.13 ( 3726) metal coordination : bond 0.00415 / 0.27 ( 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 575 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 495 time to evaluate : 0.940 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: 0.7815 (mtm110) cc_final: 0.7523 (mtm110) REVERT: A 10 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 70 LEU cc_start: 0.8545 (tp) cc_final: 0.8231 (tp) REVERT: A 71 ARG cc_start: 0.7889 (pmt170) cc_final: 0.7554 (pmt170) REVERT: A 192 ARG cc_start: 0.8462 (ptp-170) cc_final: 0.7894 (ptp-110) REVERT: A 279 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: A 403 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8532 (mmm160) REVERT: A 575 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: B 6 CYS cc_start: 0.8171 (t) cc_final: 0.7926 (m) REVERT: B 71 ARG cc_start: 0.7623 (pmm-80) cc_final: 0.7299 (pmm-80) REVERT: B 154 ASN cc_start: 0.8486 (t0) cc_final: 0.8067 (t0) REVERT: B 200 GLN cc_start: 0.8041 (pp30) cc_final: 0.7758 (pt0) REVERT: B 329 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8076 (ttt-90) REVERT: B 449 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: B 533 LEU cc_start: 0.8273 (tp) cc_final: 0.8040 (tt) REVERT: D 32 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8472 (t) REVERT: D 71 ARG cc_start: 0.8156 (ptp-110) cc_final: 0.7928 (ptp-110) REVERT: D 192 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7198 (pmm-80) REVERT: D 303 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8375 (mp0) REVERT: D 315 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: D 383 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: D 385 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8487 (mtm-85) REVERT: D 524 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: F 2 ARG cc_start: 0.7828 (mpp-170) cc_final: 0.7627 (mtm180) REVERT: F 8 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (m) REVERT: F 19 MET cc_start: 0.7956 (mtp) cc_final: 0.7533 (mtm) REVERT: F 71 ARG cc_start: 0.7486 (mtm110) cc_final: 0.7166 (mtm110) REVERT: F 164 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6398 (pp20) REVERT: F 196 MET cc_start: 0.8381 (mmp) cc_final: 0.8042 (mmp) REVERT: F 203 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 240 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: F 243 ASP cc_start: 0.8139 (t0) cc_final: 0.7794 (t70) REVERT: F 275 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8171 (ttpt) REVERT: F 526 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7282 (tm-30) REVERT: F 528 SER cc_start: 0.8894 (m) cc_final: 0.8691 (p) REVERT: E 28 ASP cc_start: 0.7935 (t0) cc_final: 0.7578 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8306 (m-80) cc_final: 0.7894 (m-10) REVERT: E 71 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7291 (mtt90) REVERT: E 130 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7395 (mt-10) REVERT: E 203 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: E 236 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7886 (ttp80) REVERT: E 246 GLN cc_start: 0.8498 (mt0) cc_final: 0.8281 (mp10) REVERT: E 517 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8706 (mtpm) REVERT: C 1 MET cc_start: 0.7968 (ppp) cc_final: 0.7655 (tmm) REVERT: C 101 LEU cc_start: 0.9049 (pp) cc_final: 0.8766 (pp) REVERT: C 196 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: C 279 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: C 308 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7998 (mm-30) REVERT: C 398 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: C 405 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8131 (mtt90) REVERT: C 528 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8299 (p) outliers start: 80 outliers final: 41 residues processed: 543 average time/residue: 0.9612 time to fit residues: 582.1601 Evaluate side-chains 533 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 477 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 248 LYS 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 38 SER Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 461 HIS 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 315 ASP Chi-restraints excluded: chain D residue 383 GLU 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 240 GLU 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 144 LEU Chi-restraints excluded: chain E residue 203 GLU 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 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 572 THR 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: 2.9990 chunk 349 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 337 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 359 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN ** 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 113 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** F 20 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 525 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081681 restraints weight = 56836.472| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.26 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29917 Z= 0.168 Angle : 0.663 14.081 40868 Z= 0.330 Chirality : 0.042 0.206 4526 Planarity : 0.005 0.084 5278 Dihedral : 8.651 166.844 4410 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.17 % Favored : 95.63 % Rotamer: Outliers : 2.56 % Allowed : 19.50 % Favored : 77.94 % 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: 0.93 (0.14), residues: 3642 helix: 1.88 (0.13), residues: 1629 sheet: -0.49 (0.22), residues: 564 loop : -0.30 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 160 TYR 0.023 0.001 TYR A 50 PHE 0.035 0.001 PHE F 125 TRP 0.044 0.001 TRP E 12 HIS 0.011 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (29899) covalent geometry : angle 0.66325 / 0.33 (40868) hydrogen bonds : bond 0.03685 / 2.52 ( 1317) hydrogen bonds : angle 4.34377 / 3.14 ( 3726) metal coordination : bond 0.00248 / 0.18 ( 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 553 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 477 time to evaluate : 1.043 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: 0.7828 (mtm110) cc_final: 0.7528 (mtm110) REVERT: A 10 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7876 (p) REVERT: A 70 LEU cc_start: 0.8591 (tp) cc_final: 0.8277 (tp) REVERT: A 71 ARG cc_start: 0.7904 (pmt170) cc_final: 0.7564 (pmt170) REVERT: A 160 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7728 (mtp-110) REVERT: A 192 ARG cc_start: 0.8458 (ptp-170) cc_final: 0.7886 (ptp-110) REVERT: A 279 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: A 403 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8556 (mmm160) REVERT: A 575 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: B 6 CYS cc_start: 0.8204 (t) cc_final: 0.7945 (m) REVERT: B 22 LEU cc_start: 0.8407 (mt) cc_final: 0.8145 (pp) REVERT: B 106 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7691 (mmtp) REVERT: B 154 ASN cc_start: 0.8530 (t0) cc_final: 0.8115 (t0) REVERT: B 329 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8084 (ttt-90) REVERT: B 449 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: D 32 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8490 (t) REVERT: D 71 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7935 (ptp-110) REVERT: D 315 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: D 383 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: D 385 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8539 (mtm-85) REVERT: D 524 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: F 2 ARG cc_start: 0.7823 (mpp-170) cc_final: 0.7594 (mtm180) REVERT: F 8 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (m) REVERT: F 19 MET cc_start: 0.7944 (mtp) cc_final: 0.7499 (mtm) REVERT: F 71 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7107 (mtm110) REVERT: F 164 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6410 (pp20) REVERT: F 203 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7399 (tm-30) REVERT: F 240 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: F 243 ASP cc_start: 0.8164 (t0) cc_final: 0.7810 (t70) REVERT: F 275 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7993 (mtpt) REVERT: F 526 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 528 SER cc_start: 0.8907 (m) cc_final: 0.8694 (p) REVERT: E 28 ASP cc_start: 0.7958 (t0) cc_final: 0.7603 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8294 (m-80) cc_final: 0.7960 (m-10) REVERT: E 80 GLU cc_start: 0.8100 (tp30) cc_final: 0.7577 (mp0) REVERT: E 130 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 203 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: E 236 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7890 (ttp80) REVERT: E 501 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8125 (mt-10) REVERT: E 517 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8692 (mtpm) REVERT: C 1 MET cc_start: 0.7981 (ppp) cc_final: 0.7567 (tmm) REVERT: C 101 LEU cc_start: 0.9055 (pp) cc_final: 0.8775 (pp) REVERT: C 196 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: C 279 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: C 308 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 398 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: C 405 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8156 (mtt90) REVERT: C 528 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8255 (p) outliers start: 76 outliers final: 43 residues processed: 518 average time/residue: 0.9959 time to fit residues: 574.5740 Evaluate side-chains 520 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 461 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR 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 248 LYS 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 38 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 461 HIS 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 315 ASP Chi-restraints excluded: chain D residue 383 GLU 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 129 CYS 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 240 GLU 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 203 GLU 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 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 528 SER 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: 0.8980 chunk 22 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN ** 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 591 GLN ** 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** F 20 GLN F 136 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082065 restraints weight = 56791.097| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3116 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29917 Z= 0.158 Angle : 0.687 14.518 40868 Z= 0.343 Chirality : 0.042 0.207 4526 Planarity : 0.005 0.098 5278 Dihedral : 8.579 164.949 4410 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 2.19 % Allowed : 20.34 % Favored : 77.47 % 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: 0.93 (0.14), residues: 3642 helix: 1.87 (0.13), residues: 1623 sheet: -0.47 (0.22), residues: 568 loop : -0.29 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 58 TYR 0.020 0.001 TYR A 50 PHE 0.034 0.001 PHE F 125 TRP 0.044 0.001 TRP E 12 HIS 0.011 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (29899) covalent geometry : angle 0.68743 / 0.34 (40868) hydrogen bonds : bond 0.03626 / 2.48 ( 1317) hydrogen bonds : angle 4.33840 / 3.14 ( 3726) metal coordination : bond 0.00211 / 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 536 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 471 time to evaluate : 1.191 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: 0.7812 (mtm110) cc_final: 0.7517 (mtm110) REVERT: A 10 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7901 (p) REVERT: A 70 LEU cc_start: 0.8589 (tp) cc_final: 0.8274 (tp) REVERT: A 71 ARG cc_start: 0.7921 (pmt170) cc_final: 0.7593 (pmt170) REVERT: A 160 ARG cc_start: 0.7908 (mtp-110) cc_final: 0.7700 (mtp-110) REVERT: A 192 ARG cc_start: 0.8451 (ptp-170) cc_final: 0.7885 (ptp-110) REVERT: A 575 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: B 6 CYS cc_start: 0.8174 (t) cc_final: 0.7923 (m) REVERT: B 22 LEU cc_start: 0.8321 (mt) cc_final: 0.7895 (pp) REVERT: B 71 ARG cc_start: 0.7587 (pmm-80) cc_final: 0.7335 (mpp80) REVERT: B 106 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7760 (mmtp) REVERT: B 154 ASN cc_start: 0.8562 (t0) cc_final: 0.8168 (t0) REVERT: B 329 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8068 (ttt-90) REVERT: B 449 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: D 2 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7432 (mtm180) REVERT: D 32 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8496 (t) REVERT: D 71 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7939 (ptp-110) REVERT: D 191 VAL cc_start: 0.8596 (t) cc_final: 0.8361 (t) REVERT: D 192 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7118 (pmm-80) REVERT: D 315 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: D 333 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: D 385 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8549 (mtm-85) REVERT: D 524 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: F 2 ARG cc_start: 0.7843 (mpp-170) cc_final: 0.7608 (mtm180) REVERT: F 8 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8390 (m) REVERT: F 10 THR cc_start: 0.8800 (m) cc_final: 0.8481 (p) REVERT: F 19 MET cc_start: 0.7956 (mtp) cc_final: 0.7503 (mtm) REVERT: F 71 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7074 (mtm110) REVERT: F 164 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6373 (pp20) REVERT: F 196 MET cc_start: 0.8435 (mmp) cc_final: 0.8225 (mmp) REVERT: F 203 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7405 (tm-30) REVERT: F 240 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: F 243 ASP cc_start: 0.8156 (t0) cc_final: 0.7812 (t70) REVERT: F 271 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7355 (tp30) REVERT: F 275 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7788 (mtmt) REVERT: F 526 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 528 SER cc_start: 0.8862 (m) cc_final: 0.8657 (p) REVERT: E 28 ASP cc_start: 0.7935 (t0) cc_final: 0.7577 (OUTLIER) REVERT: E 59 PHE cc_start: 0.8288 (m-80) cc_final: 0.7952 (m-10) REVERT: E 71 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7055 (mtm-85) REVERT: E 75 ASP cc_start: 0.7381 (p0) cc_final: 0.6411 (p0) REVERT: E 80 GLU cc_start: 0.8072 (tp30) cc_final: 0.7596 (mp0) REVERT: E 130 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7411 (mt-10) REVERT: E 203 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: E 236 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7881 (ttp80) REVERT: E 246 GLN cc_start: 0.8432 (mp10) cc_final: 0.8063 (pm20) REVERT: E 517 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8685 (mtpm) REVERT: C 1 MET cc_start: 0.8003 (ppp) cc_final: 0.7703 (tmm) REVERT: C 101 LEU cc_start: 0.9063 (pp) cc_final: 0.8791 (pp) REVERT: C 196 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: C 279 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: C 308 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 398 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: C 405 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8152 (mtt90) REVERT: C 525 GLN cc_start: 0.7346 (pp30) cc_final: 0.7003 (pp30) outliers start: 65 outliers final: 40 residues processed: 501 average time/residue: 0.9771 time to fit residues: 545.9390 Evaluate side-chains 514 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 460 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 248 LYS 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 38 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 461 HIS 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 315 ASP 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 129 CYS 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 240 GLU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 203 GLU 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 78 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 245 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 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: 0.5980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.0020 chunk 214 optimal weight: 0.0970 chunk 83 optimal weight: 0.0970 chunk 350 optimal weight: 4.9990 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 169 GLN ** 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 591 GLN F 20 GLN F 76 HIS ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS E 546 ASN C 76 HIS C 154 ASN C 282 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083762 restraints weight = 57194.933| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.28 r_work: 0.3151 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29917 Z= 0.126 Angle : 0.672 14.360 40868 Z= 0.336 Chirality : 0.041 0.217 4526 Planarity : 0.005 0.080 5278 Dihedral : 8.395 163.275 4410 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.75 % Allowed : 20.75 % Favored : 77.51 % 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: 1.02 (0.15), residues: 3642 helix: 1.95 (0.13), residues: 1620 sheet: -0.45 (0.22), residues: 573 loop : -0.25 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 58 TYR 0.020 0.001 TYR A 50 PHE 0.040 0.001 PHE B 59 TRP 0.041 0.001 TRP E 12 HIS 0.010 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (29899) covalent geometry : angle 0.67224 / 0.34 (40868) hydrogen bonds : bond 0.03279 / 2.23 ( 1317) hydrogen bonds : angle 4.27951 / 3.09 ( 3726) metal coordination : bond 0.00102 / 0.07 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13433.88 seconds wall clock time: 228 minutes 30.66 seconds (13710.66 seconds total)