Starting phenix.real_space_refine on Fri Sep 19 02:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev9_19995/09_2025/9ev9_19995.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 14635 2.51 5 N 3641 2.21 5 O 4195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22523 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4688 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4629 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3471 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4705 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4690 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.83, per 1000 atoms: 0.26 Number of scatterers: 22523 At special positions: 0 Unit cell: (139.656, 146.427, 157.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 4195 8.00 N 3641 7.00 C 14635 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 28 sheets defined 29.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.942A pdb=" N SER A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.864A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.838A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.708A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.983A pdb=" N SER B 314 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.769A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.508A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 605 through 636 Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.102A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.835A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.827A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.511A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.925A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.099A pdb=" N SER D 314 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.865A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.844A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.503A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.710A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.062A pdb=" N SER E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.800A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.517A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 605 through 637 Proline residue: E 621 - end of helix removed outlier: 3.921A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.994A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.226A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.323A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.319A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.085A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.193A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.426A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.313A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.067A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 212 removed outlier: 4.269A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.245A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.198A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.039A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.110A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.521A pdb=" N ASP D 287 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.278A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.125A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.684A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.330A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.448A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.229A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 397 through 399 removed outlier: 4.964A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2880 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: 3.91 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4652 1.33 - 1.45: 5389 1.45 - 1.57: 12887 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 23002 Sorted by residual: bond pdb=" C GLU A 326 " pdb=" N SER A 327 " ideal model delta sigma weight residual 1.329 1.271 0.058 1.43e-02 4.89e+03 1.64e+01 bond pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.62e+01 bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.61e+01 bond pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.59e+01 ... (remaining 22997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30535 1.84 - 3.67: 508 3.67 - 5.51: 103 5.51 - 7.34: 30 7.34 - 9.18: 14 Bond angle restraints: 31190 Sorted by residual: angle pdb=" N LEU B 325 " pdb=" CA LEU B 325 " pdb=" C LEU B 325 " ideal model delta sigma weight residual 109.14 118.32 -9.18 1.49e+00 4.50e-01 3.80e+01 angle pdb=" N TYR B 620 " pdb=" CA TYR B 620 " pdb=" C TYR B 620 " ideal model delta sigma weight residual 113.25 119.40 -6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" N GLU D 103 " pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 110.56 101.80 8.76 1.94e+00 2.66e-01 2.04e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.88 8.68 1.94e+00 2.66e-01 2.00e+01 ... (remaining 31185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 12841 14.37 - 28.74: 517 28.74 - 43.12: 160 43.12 - 57.49: 32 57.49 - 71.86: 10 Dihedral angle restraints: 13560 sinusoidal: 5388 harmonic: 8172 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE E 522 " pdb=" C ILE E 522 " pdb=" N PHE E 523 " pdb=" CA PHE E 523 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2966 0.056 - 0.112: 463 0.112 - 0.168: 87 0.168 - 0.224: 1 0.224 - 0.279: 9 Chirality restraints: 3526 Sorted by residual: chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 620 " pdb=" N TYR A 620 " pdb=" C TYR A 620 " pdb=" CB TYR A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3523 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 197 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C LEU B 197 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 197 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU B 198 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 326 " -0.013 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLU A 326 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 326 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 327 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 200 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO B 201 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.035 5.00e-02 4.00e+02 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1458 2.74 - 3.28: 20670 3.28 - 3.82: 34659 3.82 - 4.36: 41061 4.36 - 4.90: 73924 Nonbonded interactions: 171772 Sorted by model distance: nonbonded pdb=" OG SER E 367 " pdb=" OD1 ASP E 369 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.243 3.040 nonbonded pdb=" OG SER D 367 " pdb=" OD1 ASP D 369 " model vdw 2.253 3.040 nonbonded pdb=" OG SER C 367 " pdb=" OD1 ASP C 369 " model vdw 2.255 3.040 ... (remaining 171767 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 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 123 or (resid 124 and (name N or n \ ame CA or name C or name O or name CB )) or resid 125 through 193 or (resid 194 \ through 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 or (resid 197 through 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 or (resid 202 through 203 and (name N or name CA or name C or \ name O or name CB )) or resid 204 through 205 or (resid 206 through 208 and (nam \ e N or name CA or name C or name O or name CB )) or resid 209 through 226 or (re \ sid 227 and (name N or name CA or name C or name O or name CB )) or resid 228 th \ rough 240 or (resid 241 through 242 and (name N or name CA or name C or name O o \ r name CB )) or resid 243 through 263 or (resid 264 and (name N or name CA or na \ me C or name O or name CB )) or resid 265 through 266 or (resid 267 and (name N \ or name CA or name C or name O or name CB )) or resid 268 through 277 or (resid \ 278 through 279 and (name N or name CA or name C or name O or name CB )) or resi \ d 280 through 311 or (resid 312 through 313 and (name N or name CA or name C or \ name O or name CB )) or resid 314 through 315 or (resid 316 and (name N or name \ CA or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and \ (name N or name CA or name C or name O or name CB )) or resid 320 or (resid 321 \ through 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 902 or resid 904)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 or (resid 107 and (name N \ or name CA or name C or name O or name CB )) or resid 108 through 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB )) or resid 125 throug \ h 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or \ resid 293 through 902 or resid 904)) selection = (chain 'D' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB )) or resid 125 through 193 or (resid 194 through 195 and (name N or name CA \ or name C or name O or name CB )) or resid 196 or (resid 197 through 200 and (n \ ame N or name CA or name C or name O or name CB )) or resid 201 or (resid 202 th \ rough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 205 or (resid 206 through 208 and (name N or name CA or name C or name O \ or name CB )) or resid 209 through 226 or (resid 227 and (name N or name CA or \ name C or name O or name CB )) or resid 228 through 240 or (resid 241 through 24 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 243 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 266 or (resid 267 and (name N or name CA or name C or name O or \ name CB )) or resid 268 through 277 or (resid 278 through 279 and (name N or nam \ e CA or name C or name O or name CB )) or resid 280 through 289 or (resid 290 an \ d (name N or name CA or name C or name O or name CB )) or resid 291 or (resid 29 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 311 or (resid 312 through 313 and (name N or name CA or name C or name O or name \ CB )) or resid 314 through 315 or (resid 316 and (name N or name CA or name C o \ r name O or name CB )) or resid 317 through 318 or (resid 319 and (name N or nam \ e CA or name C or name O or name CB )) or resid 320 or (resid 321 through 322 an \ d (name N or name CA or name C or name O or name CB )) or resid 323 through 902 \ or resid 904)) selection = (chain 'E' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 193 or (resid 194 through 195 and (name N or name CA or name C or na \ me O or name CB )) or resid 196 or (resid 197 through 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 through 205 or (resid 206 throug \ h 208 and (name N or name CA or name C or name O or name CB )) or resid 209 thro \ ugh 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) o \ r resid 228 through 240 or (resid 241 through 242 and (name N or name CA or name \ C or name O or name CB )) or resid 243 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 266 or (resid 26 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 268 through \ 277 or (resid 278 through 279 and (name N or name CA or name C or name O or name \ CB )) or resid 280 through 291 or (resid 292 and (name N or name CA or name C o \ r name O or name CB )) or resid 293 through 311 or (resid 312 through 313 and (n \ ame N or name CA or name C or name O or name CB )) or resid 314 through 315 or ( \ resid 316 and (name N or name CA or name C or name O or name CB )) or resid 317 \ through 320 or (resid 321 through 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 702 or resid 704)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 21.350 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.003 0.058 23002 Z= 0.225 Angle : 0.622 9.179 31190 Z= 0.330 Chirality : 0.044 0.279 3526 Planarity : 0.004 0.064 4016 Dihedral : 9.191 71.862 8322 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 0.54 % Allowed : 3.08 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.93 (0.16), residues: 2830 helix: 1.93 (0.21), residues: 677 sheet: 0.91 (0.16), residues: 959 loop : -0.34 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 599 TYR 0.008 0.001 TYR B 517 PHE 0.011 0.001 PHE A 561 TRP 0.005 0.001 TRP D 534 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00335 (23002) covalent geometry : angle 0.62219 (31190) hydrogen bonds : bond 0.19264 ( 1045) hydrogen bonds : angle 6.36311 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 335 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 615 TRP cc_start: 0.7446 (m-10) cc_final: 0.6914 (m100) REVERT: C 347 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 460 MET cc_start: 0.7638 (mtp) cc_final: 0.7296 (mtp) REVERT: C 492 THR cc_start: 0.8719 (p) cc_final: 0.8448 (t) REVERT: C 493 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6709 (mm-30) REVERT: D 347 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7303 (mt-10) REVERT: D 471 GLN cc_start: 0.6960 (mt0) cc_final: 0.6725 (tt0) REVERT: E 420 ARG cc_start: 0.6204 (mtm110) cc_final: 0.5774 (mtp85) REVERT: E 487 TYR cc_start: 0.8086 (p90) cc_final: 0.7011 (p90) REVERT: E 622 LEU cc_start: 0.7424 (tp) cc_final: 0.7202 (mt) outliers start: 13 outliers final: 1 residues processed: 344 average time/residue: 0.7326 time to fit residues: 282.4790 Evaluate side-chains 164 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 470 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN C 272 ASN C 411 GLN D 204 HIS E 360 HIS E 411 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.213862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143353 restraints weight = 22395.655| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 5.42 r_work: 0.2854 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23002 Z= 0.221 Angle : 0.650 8.252 31190 Z= 0.349 Chirality : 0.048 0.175 3526 Planarity : 0.005 0.045 4016 Dihedral : 7.020 59.873 3301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.45 % Allowed : 8.90 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.84 (0.16), residues: 2830 helix: 1.63 (0.20), residues: 719 sheet: 0.96 (0.16), residues: 961 loop : -0.44 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 406 TYR 0.023 0.002 TYR D 517 PHE 0.020 0.003 PHE E 496 TRP 0.014 0.002 TRP C 407 HIS 0.007 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00526 (23002) covalent geometry : angle 0.64952 (31190) hydrogen bonds : bond 0.07380 ( 1045) hydrogen bonds : angle 4.90331 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.0961 (mtm) cc_final: 0.0592 (pmm) REVERT: A 68 MET cc_start: 0.4554 (ttt) cc_final: 0.4290 (ttt) REVERT: A 224 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7679 (ptp90) REVERT: A 345 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8424 (mtt-85) REVERT: A 379 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: A 420 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6962 (mtp-110) REVERT: A 562 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7952 (m) REVERT: A 566 ASP cc_start: 0.7918 (m-30) cc_final: 0.7716 (m-30) REVERT: B 347 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8982 (mt-10) REVERT: B 577 ASP cc_start: 0.8582 (m-30) cc_final: 0.8233 (m-30) REVERT: B 620 TYR cc_start: 0.7945 (m-80) cc_final: 0.7064 (m-80) REVERT: C 338 GLN cc_start: 0.8778 (tt0) cc_final: 0.8377 (tm-30) REVERT: C 345 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8700 (mtp85) REVERT: C 432 GLN cc_start: 0.8396 (mt0) cc_final: 0.7881 (mm110) REVERT: C 487 TYR cc_start: 0.8812 (p90) cc_final: 0.8590 (p90) REVERT: C 490 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: C 493 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8001 (mm-30) REVERT: C 620 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: D 58 MET cc_start: 0.2413 (tpp) cc_final: 0.1797 (mmm) REVERT: D 153 ASN cc_start: 0.7512 (t0) cc_final: 0.7286 (t0) REVERT: D 379 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: D 471 GLN cc_start: 0.7659 (mt0) cc_final: 0.7298 (pt0) REVERT: D 566 ASP cc_start: 0.6728 (m-30) cc_final: 0.6496 (m-30) REVERT: D 596 CYS cc_start: 0.8344 (t) cc_final: 0.7518 (m) REVERT: D 622 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 634 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (ttm170) REVERT: E 207 GLU cc_start: 0.7191 (tt0) cc_final: 0.6972 (mp0) REVERT: E 338 GLN cc_start: 0.8891 (tt0) cc_final: 0.8660 (tt0) REVERT: E 374 THR cc_start: 0.6111 (OUTLIER) cc_final: 0.5887 (p) REVERT: E 389 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7171 (pt0) REVERT: E 420 ARG cc_start: 0.7639 (mtm110) cc_final: 0.6772 (mtp-110) REVERT: E 512 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8835 (pttt) REVERT: E 622 LEU cc_start: 0.8242 (tp) cc_final: 0.7846 (mp) outliers start: 59 outliers final: 25 residues processed: 231 average time/residue: 0.6652 time to fit residues: 174.7728 Evaluate side-chains 198 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 562 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN D 204 HIS E 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.210322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143669 restraints weight = 22361.760| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.58 r_work: 0.3049 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23002 Z= 0.238 Angle : 0.667 8.428 31190 Z= 0.355 Chirality : 0.049 0.182 3526 Planarity : 0.005 0.062 4016 Dihedral : 7.353 59.521 3299 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.37 % Allowed : 9.85 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.58 (0.16), residues: 2830 helix: 1.47 (0.20), residues: 720 sheet: 1.02 (0.17), residues: 887 loop : -0.75 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 406 TYR 0.021 0.002 TYR D 517 PHE 0.046 0.003 PHE D 561 TRP 0.011 0.002 TRP C 407 HIS 0.005 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00582 (23002) covalent geometry : angle 0.66660 (31190) hydrogen bonds : bond 0.07799 ( 1045) hydrogen bonds : angle 4.76491 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.1322 (mtm) cc_final: 0.0915 (pmm) REVERT: A 224 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7540 (ptp90) REVERT: A 345 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8502 (mtt-85) REVERT: A 420 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6874 (mtt-85) REVERT: A 498 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5648 (mtm180) REVERT: B 82 MET cc_start: 0.5467 (pmm) cc_final: 0.5101 (pp-130) REVERT: B 347 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8991 (mt-10) REVERT: B 391 ASN cc_start: 0.8154 (t0) cc_final: 0.7599 (m110) REVERT: B 418 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8295 (p0) REVERT: C 338 GLN cc_start: 0.8850 (tt0) cc_final: 0.8460 (tt0) REVERT: C 363 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7813 (mtpt) REVERT: C 493 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8292 (mm-30) REVERT: C 620 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: D 58 MET cc_start: 0.2617 (tpp) cc_final: 0.2171 (mmm) REVERT: D 153 ASN cc_start: 0.7844 (t0) cc_final: 0.7614 (t0) REVERT: D 249 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6921 (tt) REVERT: D 363 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8575 (mttp) REVERT: D 379 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: D 622 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7909 (tt) REVERT: E 420 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7183 (mtp-110) REVERT: E 493 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: E 512 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8855 (pttt) outliers start: 81 outliers final: 29 residues processed: 223 average time/residue: 0.6930 time to fit residues: 174.9942 Evaluate side-chains 188 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 562 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.210431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139248 restraints weight = 22258.378| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.43 r_work: 0.2857 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23002 Z= 0.189 Angle : 0.599 8.582 31190 Z= 0.318 Chirality : 0.046 0.198 3526 Planarity : 0.005 0.043 4016 Dihedral : 7.006 57.927 3299 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.16 % Allowed : 10.19 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.76 (0.16), residues: 2830 helix: 1.84 (0.20), residues: 701 sheet: 1.10 (0.17), residues: 863 loop : -0.70 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 498 TYR 0.015 0.002 TYR E 517 PHE 0.043 0.002 PHE C 561 TRP 0.014 0.002 TRP A 121 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00454 (23002) covalent geometry : angle 0.59853 (31190) hydrogen bonds : bond 0.06782 ( 1045) hydrogen bonds : angle 4.56229 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 155 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.1222 (mtm) cc_final: 0.0953 (pmm) REVERT: A 158 LYS cc_start: 0.7093 (ptpt) cc_final: 0.6823 (pttp) REVERT: A 224 ARG cc_start: 0.7988 (ptp90) cc_final: 0.7453 (ptp90) REVERT: A 345 ARG cc_start: 0.8587 (mtp85) cc_final: 0.8372 (mtt-85) REVERT: A 420 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6833 (mtp-110) REVERT: A 480 GLU cc_start: 0.7573 (mp0) cc_final: 0.7297 (pm20) REVERT: B 82 MET cc_start: 0.5389 (pmm) cc_final: 0.5180 (pp-130) REVERT: B 345 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8494 (mtp180) REVERT: B 391 ASN cc_start: 0.8168 (t0) cc_final: 0.7537 (m110) REVERT: B 418 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8238 (p0) REVERT: B 620 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: C 338 GLN cc_start: 0.8822 (tt0) cc_final: 0.8457 (tt0) REVERT: C 363 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7800 (mtpt) REVERT: C 493 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8138 (mm-30) REVERT: C 620 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: D 249 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6660 (tt) REVERT: D 363 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8455 (mttp) REVERT: D 379 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: D 622 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7597 (tt) REVERT: E 338 GLN cc_start: 0.8880 (tt0) cc_final: 0.8621 (tt0) REVERT: E 389 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: E 420 ARG cc_start: 0.7847 (mtm110) cc_final: 0.6868 (mtp-110) REVERT: E 493 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: E 512 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8831 (pttt) outliers start: 76 outliers final: 40 residues processed: 208 average time/residue: 0.6484 time to fit residues: 154.1078 Evaluate side-chains 197 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 216 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 219 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 277 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.218686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155128 restraints weight = 23490.783| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.93 r_work: 0.3281 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23002 Z= 0.197 Angle : 0.606 8.136 31190 Z= 0.323 Chirality : 0.047 0.202 3526 Planarity : 0.005 0.046 4016 Dihedral : 7.129 57.833 3299 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.28 % Allowed : 10.52 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.76 (0.16), residues: 2830 helix: 1.83 (0.20), residues: 701 sheet: 0.86 (0.17), residues: 941 loop : -0.58 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 406 TYR 0.016 0.002 TYR E 517 PHE 0.054 0.002 PHE B 561 TRP 0.011 0.002 TRP A 121 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00476 (23002) covalent geometry : angle 0.60621 (31190) hydrogen bonds : bond 0.06990 ( 1045) hydrogen bonds : angle 4.56951 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 147 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.1151 (mtm) cc_final: 0.0882 (pmm) REVERT: A 158 LYS cc_start: 0.7216 (ptpt) cc_final: 0.6991 (pttp) REVERT: A 224 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7670 (ptp90) REVERT: A 356 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8579 (mtpp) REVERT: A 420 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6895 (mtp-110) REVERT: A 480 GLU cc_start: 0.7745 (mp0) cc_final: 0.7498 (pm20) REVERT: A 498 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5852 (ptt180) REVERT: B 391 ASN cc_start: 0.8163 (t0) cc_final: 0.7583 (m110) REVERT: B 418 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8251 (p0) REVERT: B 620 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: C 235 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6455 (tp) REVERT: C 338 GLN cc_start: 0.8878 (tt0) cc_final: 0.8503 (tt0) REVERT: C 363 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7970 (mtpt) REVERT: C 379 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 493 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8187 (mm-30) REVERT: C 620 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: D 249 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7048 (tt) REVERT: D 281 GLU cc_start: 0.7389 (mp0) cc_final: 0.6981 (mt-10) REVERT: D 363 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8576 (mtmt) REVERT: D 379 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: D 622 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7827 (tt) REVERT: E 58 MET cc_start: -0.1877 (mpp) cc_final: -0.2301 (mmt) REVERT: E 389 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: E 420 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7083 (mtp-110) REVERT: E 493 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: E 512 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8783 (pttt) outliers start: 79 outliers final: 46 residues processed: 206 average time/residue: 0.6070 time to fit residues: 143.4187 Evaluate side-chains 205 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 256 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.216861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152790 restraints weight = 23675.559| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.97 r_work: 0.3262 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 23002 Z= 0.277 Angle : 0.700 8.732 31190 Z= 0.372 Chirality : 0.051 0.204 3526 Planarity : 0.005 0.067 4016 Dihedral : 7.908 59.458 3299 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.62 % Allowed : 10.52 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.41 (0.16), residues: 2830 helix: 1.43 (0.19), residues: 709 sheet: 0.65 (0.16), residues: 955 loop : -0.73 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 406 TYR 0.020 0.003 TYR E 517 PHE 0.060 0.003 PHE B 561 TRP 0.015 0.002 TRP A 121 HIS 0.009 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00686 (23002) covalent geometry : angle 0.69980 (31190) hydrogen bonds : bond 0.08419 ( 1045) hydrogen bonds : angle 4.82302 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 147 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.1062 (mtm) cc_final: 0.0776 (pmm) REVERT: A 82 MET cc_start: 0.5230 (ptm) cc_final: 0.4831 (ptp) REVERT: A 224 ARG cc_start: 0.8202 (ptp90) cc_final: 0.7909 (ptp90) REVERT: A 420 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6820 (mtp-110) REVERT: A 480 GLU cc_start: 0.7854 (mp0) cc_final: 0.7506 (pm20) REVERT: A 498 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5861 (ptt180) REVERT: B 391 ASN cc_start: 0.8202 (t0) cc_final: 0.7581 (m110) REVERT: B 418 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 564 SER cc_start: 0.8335 (t) cc_final: 0.8063 (m) REVERT: C 235 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6398 (tp) REVERT: C 299 VAL cc_start: 0.5580 (OUTLIER) cc_final: 0.5301 (t) REVERT: C 338 GLN cc_start: 0.8890 (tt0) cc_final: 0.8530 (tm-30) REVERT: C 363 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8077 (mtpp) REVERT: C 379 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: C 493 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8251 (mm-30) REVERT: C 620 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: D 249 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7199 (tt) REVERT: D 281 GLU cc_start: 0.7493 (mp0) cc_final: 0.7065 (mt-10) REVERT: D 363 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8519 (mttp) REVERT: D 379 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: D 622 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7961 (tt) REVERT: E 58 MET cc_start: -0.1644 (mpp) cc_final: -0.1898 (mtt) REVERT: E 389 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: E 420 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7274 (mtp-110) REVERT: E 512 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8803 (pttt) REVERT: E 596 CYS cc_start: 0.8585 (t) cc_final: 0.8026 (m) outliers start: 87 outliers final: 51 residues processed: 210 average time/residue: 0.6234 time to fit residues: 150.4885 Evaluate side-chains 206 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 220 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 276 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 338 GLN C 432 GLN D 204 HIS D 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.219911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157215 restraints weight = 23758.758| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 4.99 r_work: 0.3301 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23002 Z= 0.135 Angle : 0.541 8.271 31190 Z= 0.287 Chirality : 0.044 0.192 3526 Planarity : 0.004 0.044 4016 Dihedral : 7.057 58.099 3299 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.74 % Allowed : 11.48 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.83 (0.16), residues: 2830 helix: 2.07 (0.20), residues: 702 sheet: 0.80 (0.17), residues: 951 loop : -0.58 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.013 0.002 TYR D 542 PHE 0.046 0.002 PHE D 561 TRP 0.010 0.001 TRP A 121 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00306 (23002) covalent geometry : angle 0.54120 (31190) hydrogen bonds : bond 0.05701 ( 1045) hydrogen bonds : angle 4.42251 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.1204 (mtm) cc_final: 0.0929 (pmm) REVERT: A 158 LYS cc_start: 0.7549 (pptt) cc_final: 0.7279 (pptt) REVERT: A 199 ILE cc_start: 0.4637 (OUTLIER) cc_final: 0.4233 (pp) REVERT: A 224 ARG cc_start: 0.8184 (ptp90) cc_final: 0.7695 (ptp90) REVERT: A 247 LEU cc_start: 0.6977 (tp) cc_final: 0.6393 (tp) REVERT: A 420 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7047 (mtp-110) REVERT: A 480 GLU cc_start: 0.7796 (mp0) cc_final: 0.7520 (pm20) REVERT: A 498 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5785 (pmt170) REVERT: B 391 ASN cc_start: 0.8195 (t0) cc_final: 0.7574 (m110) REVERT: B 418 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8315 (p0) REVERT: B 620 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6299 (t80) REVERT: C 235 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6393 (tp) REVERT: C 338 GLN cc_start: 0.8837 (tt0) cc_final: 0.8472 (tt0) REVERT: C 363 LYS cc_start: 0.8224 (mtmt) cc_final: 0.8007 (mtpp) REVERT: C 493 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8122 (mm-30) REVERT: C 620 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: D 206 GLN cc_start: 0.6751 (tt0) cc_final: 0.6460 (tt0) REVERT: D 363 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8547 (mtmt) REVERT: D 379 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: D 476 GLN cc_start: 0.7263 (pt0) cc_final: 0.6865 (pt0) REVERT: D 622 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7787 (tt) REVERT: E 58 MET cc_start: -0.1641 (mpp) cc_final: -0.1850 (mtt) REVERT: E 338 GLN cc_start: 0.8964 (tt0) cc_final: 0.8727 (tt0) REVERT: E 389 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6773 (pt0) REVERT: E 420 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7058 (mtp-110) outliers start: 66 outliers final: 32 residues processed: 206 average time/residue: 0.6102 time to fit residues: 144.4616 Evaluate side-chains 187 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 633 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 265 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 233 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS E 471 GLN E 560 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.218369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155897 restraints weight = 23613.266| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.82 r_work: 0.3280 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23002 Z= 0.187 Angle : 0.593 8.686 31190 Z= 0.315 Chirality : 0.046 0.166 3526 Planarity : 0.004 0.044 4016 Dihedral : 7.120 54.861 3299 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 12.27 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.70 (0.16), residues: 2830 helix: 1.91 (0.20), residues: 703 sheet: 0.76 (0.17), residues: 944 loop : -0.64 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 521 TYR 0.016 0.002 TYR D 542 PHE 0.059 0.002 PHE B 561 TRP 0.011 0.002 TRP A 121 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00450 (23002) covalent geometry : angle 0.59326 (31190) hydrogen bonds : bond 0.06765 ( 1045) hydrogen bonds : angle 4.52117 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.0977 (mtm) cc_final: 0.0690 (pmm) REVERT: A 158 LYS cc_start: 0.7601 (pptt) cc_final: 0.7246 (pptt) REVERT: A 199 ILE cc_start: 0.4570 (OUTLIER) cc_final: 0.4235 (pp) REVERT: A 224 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7718 (ptp90) REVERT: A 247 LEU cc_start: 0.6970 (tp) cc_final: 0.6350 (tp) REVERT: A 420 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6882 (mtp-110) REVERT: A 480 GLU cc_start: 0.7814 (mp0) cc_final: 0.7530 (pm20) REVERT: A 498 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5805 (pmt170) REVERT: B 391 ASN cc_start: 0.8204 (t0) cc_final: 0.7594 (m110) REVERT: B 418 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8221 (p0) REVERT: B 620 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6430 (t80) REVERT: C 235 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6397 (tp) REVERT: C 338 GLN cc_start: 0.8860 (tt0) cc_final: 0.8500 (tm-30) REVERT: C 363 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8062 (mtpp) REVERT: C 379 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: C 493 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8172 (mm-30) REVERT: C 620 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: D 206 GLN cc_start: 0.6717 (tt0) cc_final: 0.6426 (tt0) REVERT: D 363 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8552 (mtmt) REVERT: D 379 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: D 476 GLN cc_start: 0.7301 (pt0) cc_final: 0.6959 (pt0) REVERT: D 622 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7823 (tt) REVERT: E 58 MET cc_start: -0.1493 (mpp) cc_final: -0.1702 (mtt) REVERT: E 389 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: E 420 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7139 (mtp-110) REVERT: E 493 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7953 (mt-10) outliers start: 57 outliers final: 37 residues processed: 188 average time/residue: 0.6170 time to fit residues: 132.6375 Evaluate side-chains 191 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain E residue 633 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 215 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 259 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 274 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.208544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133093 restraints weight = 22332.518| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 5.46 r_work: 0.2868 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23002 Z= 0.137 Angle : 0.536 8.494 31190 Z= 0.284 Chirality : 0.044 0.157 3526 Planarity : 0.004 0.045 4016 Dihedral : 6.685 57.606 3299 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.41 % Allowed : 12.35 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.87 (0.16), residues: 2830 helix: 2.12 (0.20), residues: 702 sheet: 0.82 (0.17), residues: 954 loop : -0.57 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 521 TYR 0.013 0.002 TYR D 542 PHE 0.038 0.002 PHE D 561 TRP 0.009 0.001 TRP A 121 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00315 (23002) covalent geometry : angle 0.53603 (31190) hydrogen bonds : bond 0.05583 ( 1045) hydrogen bonds : angle 4.33251 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.1043 (mtm) cc_final: 0.0812 (pmm) REVERT: A 158 LYS cc_start: 0.7362 (pptt) cc_final: 0.7002 (pptt) REVERT: A 199 ILE cc_start: 0.4482 (OUTLIER) cc_final: 0.4142 (pp) REVERT: A 224 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7436 (ptp90) REVERT: A 247 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6169 (tp) REVERT: A 281 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 420 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6879 (mtp-110) REVERT: A 480 GLU cc_start: 0.7627 (mp0) cc_final: 0.7329 (pm20) REVERT: B 391 ASN cc_start: 0.8230 (t0) cc_final: 0.7555 (m110) REVERT: B 418 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8185 (p0) REVERT: B 620 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6188 (t80) REVERT: C 235 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6223 (tp) REVERT: C 338 GLN cc_start: 0.8803 (tt0) cc_final: 0.8429 (tt0) REVERT: C 363 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7977 (mtpp) REVERT: C 379 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: C 493 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8123 (mm-30) REVERT: C 620 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: D 82 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.3714 (ptm) REVERT: D 206 GLN cc_start: 0.6183 (tt0) cc_final: 0.5831 (tt0) REVERT: D 281 GLU cc_start: 0.7092 (mp0) cc_final: 0.6692 (mt-10) REVERT: D 363 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8526 (mtmt) REVERT: D 379 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: D 476 GLN cc_start: 0.7293 (pt0) cc_final: 0.6916 (pt0) REVERT: D 622 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7641 (tt) REVERT: E 58 MET cc_start: -0.1539 (mpp) cc_final: -0.1807 (mtt) REVERT: E 338 GLN cc_start: 0.8864 (tt0) cc_final: 0.8603 (tt0) REVERT: E 389 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6636 (pt0) REVERT: E 420 ARG cc_start: 0.7991 (mtm110) cc_final: 0.6925 (mtp-110) REVERT: E 493 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: E 622 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7893 (mp) outliers start: 58 outliers final: 34 residues processed: 189 average time/residue: 0.6272 time to fit residues: 136.4228 Evaluate side-chains 193 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 193 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS E 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.207705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131048 restraints weight = 22370.997| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 5.68 r_work: 0.2853 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23002 Z= 0.155 Angle : 0.558 8.483 31190 Z= 0.296 Chirality : 0.045 0.164 3526 Planarity : 0.004 0.045 4016 Dihedral : 6.690 59.042 3299 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.20 % Allowed : 12.64 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.83 (0.16), residues: 2830 helix: 2.07 (0.20), residues: 702 sheet: 0.83 (0.17), residues: 941 loop : -0.60 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 521 TYR 0.015 0.002 TYR D 517 PHE 0.064 0.002 PHE B 561 TRP 0.010 0.001 TRP A 121 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00363 (23002) covalent geometry : angle 0.55797 (31190) hydrogen bonds : bond 0.06099 ( 1045) hydrogen bonds : angle 4.38269 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.1025 (mtm) cc_final: 0.0805 (pmm) REVERT: A 158 LYS cc_start: 0.7361 (pptt) cc_final: 0.7047 (pptt) REVERT: A 199 ILE cc_start: 0.4523 (OUTLIER) cc_final: 0.4165 (pp) REVERT: A 224 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7480 (ptp90) REVERT: A 230 ASP cc_start: 0.7080 (m-30) cc_final: 0.6533 (p0) REVERT: A 247 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6101 (tp) REVERT: A 281 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7500 (mp0) REVERT: A 370 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 420 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6933 (mtp-110) REVERT: A 480 GLU cc_start: 0.7639 (mp0) cc_final: 0.7335 (pm20) REVERT: B 391 ASN cc_start: 0.8227 (t0) cc_final: 0.7573 (m110) REVERT: B 418 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8148 (p0) REVERT: B 620 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6192 (t80) REVERT: C 235 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6217 (tp) REVERT: C 338 GLN cc_start: 0.8844 (tt0) cc_final: 0.8444 (tm-30) REVERT: C 363 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7986 (mtpp) REVERT: C 379 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: C 493 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8135 (mm-30) REVERT: C 620 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: D 82 MET cc_start: 0.4534 (OUTLIER) cc_final: 0.3766 (ptm) REVERT: D 206 GLN cc_start: 0.6232 (tt0) cc_final: 0.5842 (tt0) REVERT: D 281 GLU cc_start: 0.7113 (mp0) cc_final: 0.6726 (mt-10) REVERT: D 379 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: D 476 GLN cc_start: 0.7275 (pt0) cc_final: 0.6947 (pt0) REVERT: D 622 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7676 (tt) REVERT: E 58 MET cc_start: -0.1502 (mpp) cc_final: -0.1752 (mtt) REVERT: E 389 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: E 420 ARG cc_start: 0.8010 (mtm110) cc_final: 0.6950 (mtp-110) REVERT: E 493 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7947 (mt-10) outliers start: 53 outliers final: 36 residues processed: 182 average time/residue: 0.6552 time to fit residues: 137.1742 Evaluate side-chains 189 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 6 optimal weight: 30.0000 chunk 260 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 223 optimal weight: 40.0000 chunk 280 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS E 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.209490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135852 restraints weight = 22401.993| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 5.21 r_work: 0.2876 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23002 Z= 0.118 Angle : 0.512 8.381 31190 Z= 0.270 Chirality : 0.043 0.155 3526 Planarity : 0.004 0.046 4016 Dihedral : 6.316 59.845 3299 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 12.77 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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 aren not related in a simple way. whole: 0.99 (0.16), residues: 2830 helix: 2.32 (0.20), residues: 695 sheet: 0.74 (0.17), residues: 975 loop : -0.41 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 521 TYR 0.013 0.001 TYR E 542 PHE 0.031 0.002 PHE D 561 TRP 0.008 0.001 TRP A 121 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00264 (23002) covalent geometry : angle 0.51199 (31190) hydrogen bonds : bond 0.05062 ( 1045) hydrogen bonds : angle 4.22748 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7885.60 seconds wall clock time: 134 minutes 41.56 seconds (8081.56 seconds total)