Starting phenix.real_space_refine on Mon Jun 23 00:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172.map" model { file = "/net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhw_29172/06_2025/8fhw_29172_neut_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.181 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 8772 2.51 5 N 2312 2.21 5 O 2488 1.98 5 H 12776 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26420 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 6553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6553 Classifications: {'peptide': 432} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.68, per 1000 atoms: 0.48 Number of scatterers: 26420 At special positions: 0 Unit cell: (115.56, 104.76, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 12 15.00 O 2488 8.00 N 2312 7.00 C 8772 6.00 H 12776 1.00 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: 7.12 Conformation dependent library (CDL) restraints added in 2.1 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 53.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.571A pdb=" N HIS A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.714A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.635A pdb=" N ALA A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 390 through 404 removed outlier: 3.612A pdb=" N ARG A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 456 through 478 removed outlier: 3.580A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 504 removed outlier: 3.545A pdb=" N ALA A 504 " --> pdb=" O MET A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 4.264A pdb=" N TYR A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.571A pdb=" N HIS B 155 " --> pdb=" O TRP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 185 removed outlier: 3.714A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.634A pdb=" N ALA B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 390 through 404 removed outlier: 3.612A pdb=" N ARG B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 456 through 478 removed outlier: 3.579A pdb=" N GLN B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 504 removed outlier: 3.544A pdb=" N ALA B 504 " --> pdb=" O MET B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 526 removed outlier: 4.265A pdb=" N TYR B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 571 through 589 Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 149 through 155 removed outlier: 3.572A pdb=" N HIS C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 185 removed outlier: 3.716A pdb=" N LEU C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 339 through 354 removed outlier: 3.635A pdb=" N ALA C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 390 through 404 removed outlier: 3.611A pdb=" N ARG C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 456 through 478 removed outlier: 3.579A pdb=" N GLN C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 504 removed outlier: 3.545A pdb=" N ALA C 504 " --> pdb=" O MET C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 526 removed outlier: 4.264A pdb=" N TYR C 521 " --> pdb=" O ASN C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 571 through 589 Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 141 through 149 Processing helix chain 'D' and resid 149 through 155 removed outlier: 3.571A pdb=" N HIS D 155 " --> pdb=" O TRP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 185 removed outlier: 3.715A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 339 through 354 removed outlier: 3.635A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 389 Processing helix chain 'D' and resid 390 through 404 removed outlier: 3.611A pdb=" N ARG D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 437 through 440 Processing helix chain 'D' and resid 456 through 478 removed outlier: 3.579A pdb=" N GLN D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 504 removed outlier: 3.545A pdb=" N ALA D 504 " --> pdb=" O MET D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 526 removed outlier: 4.264A pdb=" N TYR D 521 " --> pdb=" O ASN D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 571 through 589 Processing helix chain 'D' and resid 590 through 604 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.522A pdb=" N LEU A 334 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 362 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 488 removed outlier: 8.091A pdb=" N HIS A 486 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 445 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET A 488 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN A 447 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS A 408 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 446 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 410 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 448 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 412 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 450 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASP A 414 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 409 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 508 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 411 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N CYS A 507 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER A 537 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET A 534 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 552 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 536 " --> pdb=" O ILE A 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.522A pdb=" N LEU B 334 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 362 " --> pdb=" O GLN B 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 485 through 488 removed outlier: 8.090A pdb=" N HIS B 486 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 445 " --> pdb=" O HIS B 486 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET B 488 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 447 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS B 408 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 446 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 410 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 448 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 412 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE B 450 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP B 414 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 409 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU B 508 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 411 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N CYS B 507 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER B 537 " --> pdb=" O CYS B 507 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET B 534 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE B 552 " --> pdb=" O MET B 534 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 536 " --> pdb=" O ILE B 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.523A pdb=" N LEU C 334 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 362 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 485 through 488 removed outlier: 8.091A pdb=" N HIS C 486 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 445 " --> pdb=" O HIS C 486 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET C 488 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN C 447 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS C 408 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 446 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 410 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU C 448 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 412 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 450 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASP C 414 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 409 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU C 508 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 411 " --> pdb=" O LEU C 508 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS C 507 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER C 537 " --> pdb=" O CYS C 507 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET C 534 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE C 552 " --> pdb=" O MET C 534 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 536 " --> pdb=" O ILE C 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.523A pdb=" N LEU D 334 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 362 " --> pdb=" O GLN D 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 485 through 488 removed outlier: 8.091A pdb=" N HIS D 486 " --> pdb=" O VAL D 443 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 445 " --> pdb=" O HIS D 486 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET D 488 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN D 447 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS D 408 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL D 446 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 410 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU D 448 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY D 412 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 450 " --> pdb=" O GLY D 412 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASP D 414 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 409 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU D 508 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 411 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N CYS D 507 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER D 537 " --> pdb=" O CYS D 507 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET D 534 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE D 552 " --> pdb=" O MET D 534 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 536 " --> pdb=" O ILE D 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 684 hydrogen bonds defined for protein. 2004 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: 10.42 Time building geometry restraints manager: 8.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12756 1.03 - 1.22: 27 1.22 - 1.42: 5981 1.42 - 1.61: 7884 1.61 - 1.80: 104 Bond restraints: 26752 Sorted by residual: bond pdb=" O1B UDP B 701 " pdb=" PB UDP B 701 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.00e-02 1.00e+04 2.45e+01 bond pdb=" O1B UDP D 701 " pdb=" PB UDP D 701 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.00e-02 1.00e+04 2.39e+01 bond pdb=" C1 G6P D 702 " pdb=" O5 G6P D 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 G6P C 702 " pdb=" O5 G6P C 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 G6P B 702 " pdb=" O5 G6P B 702 " ideal model delta sigma weight residual 1.401 1.492 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 26747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 47555 1.84 - 3.68: 309 3.68 - 5.52: 76 5.52 - 7.36: 12 7.36 - 9.20: 8 Bond angle restraints: 47960 Sorted by residual: angle pdb=" O1B UDP D 701 " pdb=" PB UDP D 701 " pdb=" O3A UDP D 701 " ideal model delta sigma weight residual 102.95 112.15 -9.20 1.00e+00 1.00e+00 8.46e+01 angle pdb=" O1B UDP B 701 " pdb=" PB UDP B 701 " pdb=" O3A UDP B 701 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.43e+01 angle pdb=" O3A UDP B 701 " pdb=" PB UDP B 701 " pdb=" O3B UDP B 701 " ideal model delta sigma weight residual 112.01 103.01 9.00 1.00e+00 1.00e+00 8.11e+01 angle pdb=" O3A UDP D 701 " pdb=" PB UDP D 701 " pdb=" O3B UDP D 701 " ideal model delta sigma weight residual 112.01 103.09 8.92 1.00e+00 1.00e+00 7.96e+01 angle pdb=" O5' UDP A 701 " pdb=" PA UDP A 701 " pdb=" O1A UDP A 701 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 ... (remaining 47955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11550 17.89 - 35.78: 955 35.78 - 53.67: 251 53.67 - 71.56: 74 71.56 - 89.45: 14 Dihedral angle restraints: 12844 sinusoidal: 6824 harmonic: 6020 Sorted by residual: dihedral pdb=" CA MET A 500 " pdb=" C MET A 500 " pdb=" N TYR A 501 " pdb=" CA TYR A 501 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET B 500 " pdb=" C MET B 500 " pdb=" N TYR B 501 " pdb=" CA TYR B 501 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET C 500 " pdb=" C MET C 500 " pdb=" N TYR C 501 " pdb=" CA TYR C 501 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 12841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1863 0.064 - 0.128: 258 0.128 - 0.192: 11 0.192 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C1 G6P C 702 " pdb=" C2 G6P C 702 " pdb=" O1 G6P C 702 " pdb=" O5 G6P C 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 G6P B 702 " pdb=" C2 G6P B 702 " pdb=" O1 G6P B 702 " pdb=" O5 G6P B 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C1 G6P A 702 " pdb=" C2 G6P A 702 " pdb=" O1 G6P A 702 " pdb=" O5 G6P A 702 " both_signs ideal model delta sigma weight residual False -2.03 -2.35 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2133 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 422 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO A 423 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 422 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 423 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 422 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 423 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.018 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 668 2.13 - 2.75: 47436 2.75 - 3.37: 73874 3.37 - 3.98: 97708 3.98 - 4.60: 155023 Nonbonded interactions: 374709 Sorted by model distance: nonbonded pdb=" HG SER A 312 " pdb=" HG SER D 312 " model vdw 1.517 2.100 nonbonded pdb=" HG SER B 312 " pdb=" HG SER C 312 " model vdw 1.524 2.100 nonbonded pdb=" HE ARG D 453 " pdb=" O3P G6P D 702 " model vdw 1.638 2.450 nonbonded pdb=" HE ARG C 453 " pdb=" O2P G6P C 702 " model vdw 1.638 2.450 nonbonded pdb=" HE ARG B 453 " pdb=" O3P G6P B 702 " model vdw 1.638 2.450 ... (remaining 374704 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.000 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: 0.460 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 56.760 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.006 0.091 13976 Z= 0.274 Angle : 0.641 9.198 19028 Z= 0.354 Chirality : 0.046 0.319 2136 Planarity : 0.003 0.032 2392 Dihedral : 14.679 89.454 5080 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.81 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1680 helix: 0.96 (0.17), residues: 852 sheet: 0.39 (0.36), residues: 212 loop : -1.73 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.002 PHE D 310 TYR 0.010 0.002 TYR D 589 ARG 0.006 0.001 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.17354 ( 684) hydrogen bonds : angle 6.15492 ( 2004) covalent geometry : bond 0.00582 (13976) covalent geometry : angle 0.64135 (19028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.6419 time to fit residues: 94.7213 Evaluate side-chains 76 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS D 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107514 restraints weight = 57475.731| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.38 r_work: 0.3331 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13976 Z= 0.163 Angle : 0.519 4.777 19028 Z= 0.274 Chirality : 0.043 0.153 2136 Planarity : 0.004 0.033 2392 Dihedral : 7.319 88.688 2092 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.70 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1680 helix: 1.07 (0.17), residues: 884 sheet: 0.25 (0.35), residues: 220 loop : -1.70 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 168 HIS 0.004 0.001 HIS A 167 PHE 0.011 0.001 PHE C 310 TYR 0.013 0.001 TYR B 589 ARG 0.003 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 684) hydrogen bonds : angle 4.90200 ( 2004) covalent geometry : bond 0.00376 (13976) covalent geometry : angle 0.51852 (19028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.371 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.8756 (tpt) cc_final: 0.8482 (tpt) REVERT: B 534 MET cc_start: 0.8742 (tpt) cc_final: 0.8516 (tpt) REVERT: C 534 MET cc_start: 0.8755 (tpt) cc_final: 0.8480 (tpt) REVERT: D 534 MET cc_start: 0.8756 (tpt) cc_final: 0.8480 (tpt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.5300 time to fit residues: 65.6335 Evaluate side-chains 76 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 24 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS D 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112337 restraints weight = 55088.130| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.25 r_work: 0.3421 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13976 Z= 0.220 Angle : 0.549 4.827 19028 Z= 0.287 Chirality : 0.044 0.155 2136 Planarity : 0.004 0.035 2392 Dihedral : 7.297 87.148 2092 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.15 % Allowed : 9.24 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1680 helix: 0.93 (0.17), residues: 888 sheet: 0.18 (0.34), residues: 220 loop : -1.78 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 168 HIS 0.003 0.001 HIS C 141 PHE 0.014 0.002 PHE A 100 TYR 0.016 0.002 TYR B 589 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 684) hydrogen bonds : angle 4.83043 ( 2004) covalent geometry : bond 0.00534 (13976) covalent geometry : angle 0.54919 (19028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 2.235 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 85 average time/residue: 0.5437 time to fit residues: 70.3977 Evaluate side-chains 84 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114278 restraints weight = 55105.028| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.27 r_work: 0.3451 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13976 Z= 0.143 Angle : 0.492 4.592 19028 Z= 0.257 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.045 2392 Dihedral : 7.007 86.688 2092 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.93 % Allowed : 9.89 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1680 helix: 1.33 (0.17), residues: 888 sheet: 0.16 (0.34), residues: 220 loop : -1.69 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.007 0.001 HIS C 141 PHE 0.010 0.001 PHE A 310 TYR 0.012 0.001 TYR C 589 ARG 0.006 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 684) hydrogen bonds : angle 4.59139 ( 2004) covalent geometry : bond 0.00332 (13976) covalent geometry : angle 0.49176 (19028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: A 351 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8443 (t) REVERT: B 351 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (t) REVERT: C 351 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8447 (t) REVERT: D 351 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8444 (t) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.5659 time to fit residues: 73.2505 Evaluate side-chains 86 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS D 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.123838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112605 restraints weight = 55762.712| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.29 r_work: 0.3406 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13976 Z= 0.207 Angle : 0.535 5.257 19028 Z= 0.279 Chirality : 0.043 0.154 2136 Planarity : 0.004 0.034 2392 Dihedral : 7.087 85.042 2092 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.93 % Allowed : 9.96 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1680 helix: 1.15 (0.17), residues: 892 sheet: 0.09 (0.33), residues: 220 loop : -1.74 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 168 HIS 0.002 0.001 HIS A 198 PHE 0.013 0.002 PHE C 100 TYR 0.015 0.002 TYR C 589 ARG 0.006 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 684) hydrogen bonds : angle 4.67695 ( 2004) covalent geometry : bond 0.00504 (13976) covalent geometry : angle 0.53455 (19028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8414 (t) REVERT: B 351 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 351 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8415 (t) REVERT: D 351 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8415 (t) outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.4978 time to fit residues: 79.3399 Evaluate side-chains 96 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111945 restraints weight = 55508.297| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.27 r_work: 0.3397 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13976 Z= 0.228 Angle : 0.551 5.047 19028 Z= 0.288 Chirality : 0.044 0.155 2136 Planarity : 0.004 0.035 2392 Dihedral : 7.178 84.178 2092 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.43 % Allowed : 11.46 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1680 helix: 1.05 (0.17), residues: 892 sheet: 0.06 (0.33), residues: 220 loop : -1.76 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 168 HIS 0.006 0.001 HIS C 141 PHE 0.015 0.002 PHE B 100 TYR 0.016 0.002 TYR C 589 ARG 0.006 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 684) hydrogen bonds : angle 4.71930 ( 2004) covalent geometry : bond 0.00554 (13976) covalent geometry : angle 0.55078 (19028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8425 (t) REVERT: B 351 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8423 (t) REVERT: C 351 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8421 (t) REVERT: D 351 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8426 (t) outliers start: 20 outliers final: 12 residues processed: 100 average time/residue: 0.4546 time to fit residues: 76.5758 Evaluate side-chains 92 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114911 restraints weight = 54918.159| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.28 r_work: 0.3436 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13976 Z= 0.121 Angle : 0.468 4.569 19028 Z= 0.242 Chirality : 0.042 0.154 2136 Planarity : 0.004 0.034 2392 Dihedral : 6.858 85.321 2092 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.86 % Allowed : 11.75 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1680 helix: 1.59 (0.17), residues: 892 sheet: 0.04 (0.33), residues: 220 loop : -1.61 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 168 HIS 0.002 0.001 HIS B 198 PHE 0.009 0.001 PHE B 310 TYR 0.010 0.001 TYR D 589 ARG 0.006 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 684) hydrogen bonds : angle 4.43101 ( 2004) covalent geometry : bond 0.00282 (13976) covalent geometry : angle 0.46757 (19028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.967 Fit side-chains REVERT: A 351 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8335 (t) REVERT: B 351 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8340 (t) REVERT: C 351 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8344 (t) REVERT: D 351 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8343 (t) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.5495 time to fit residues: 86.4095 Evaluate side-chains 92 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 112 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112621 restraints weight = 55163.596| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.25 r_work: 0.3405 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13976 Z= 0.182 Angle : 0.508 4.529 19028 Z= 0.264 Chirality : 0.043 0.153 2136 Planarity : 0.004 0.033 2392 Dihedral : 6.960 83.584 2092 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.22 % Allowed : 11.10 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1680 helix: 1.49 (0.17), residues: 892 sheet: 0.05 (0.34), residues: 220 loop : -1.62 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.003 0.001 HIS B 141 PHE 0.011 0.002 PHE B 384 TYR 0.013 0.002 TYR D 589 ARG 0.005 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 684) hydrogen bonds : angle 4.51893 ( 2004) covalent geometry : bond 0.00441 (13976) covalent geometry : angle 0.50809 (19028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8407 (t) REVERT: B 351 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8407 (t) REVERT: C 351 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8410 (t) REVERT: D 351 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8412 (t) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.4298 time to fit residues: 72.0535 Evaluate side-chains 101 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 74 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111532 restraints weight = 55689.522| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.27 r_work: 0.3386 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13976 Z= 0.226 Angle : 0.546 4.900 19028 Z= 0.285 Chirality : 0.044 0.152 2136 Planarity : 0.004 0.033 2392 Dihedral : 7.193 82.896 2092 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.72 % Allowed : 10.60 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1680 helix: 1.22 (0.17), residues: 892 sheet: 0.00 (0.34), residues: 220 loop : -1.73 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 168 HIS 0.004 0.001 HIS D 141 PHE 0.013 0.002 PHE C 100 TYR 0.016 0.002 TYR C 589 ARG 0.005 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 684) hydrogen bonds : angle 4.62672 ( 2004) covalent geometry : bond 0.00552 (13976) covalent geometry : angle 0.54633 (19028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8423 (t) REVERT: B 351 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8421 (t) REVERT: C 351 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8424 (t) REVERT: D 351 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (t) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.4678 time to fit residues: 82.6514 Evaluate side-chains 101 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 96 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114916 restraints weight = 54945.682| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.23 r_work: 0.3437 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13976 Z= 0.118 Angle : 0.462 4.548 19028 Z= 0.239 Chirality : 0.042 0.155 2136 Planarity : 0.004 0.034 2392 Dihedral : 6.948 84.375 2092 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.15 % Allowed : 11.17 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1680 helix: 1.68 (0.17), residues: 892 sheet: 0.12 (0.33), residues: 248 loop : -1.69 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.000 HIS A 198 PHE 0.008 0.001 PHE A 310 TYR 0.010 0.001 TYR D 589 ARG 0.005 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 684) hydrogen bonds : angle 4.35509 ( 2004) covalent geometry : bond 0.00276 (13976) covalent geometry : angle 0.46237 (19028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 434 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 2.021 Fit side-chains REVERT: A 333 ASP cc_start: 0.7910 (m-30) cc_final: 0.7701 (m-30) REVERT: A 351 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8337 (t) REVERT: B 333 ASP cc_start: 0.7903 (m-30) cc_final: 0.7696 (m-30) REVERT: B 351 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 333 ASP cc_start: 0.7920 (m-30) cc_final: 0.7714 (m-30) REVERT: C 351 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8340 (t) REVERT: D 333 ASP cc_start: 0.7912 (m-30) cc_final: 0.7704 (m-30) REVERT: D 351 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (t) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.4365 time to fit residues: 75.9546 Evaluate side-chains 104 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114087 restraints weight = 55295.798| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.27 r_work: 0.3426 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13976 Z= 0.135 Angle : 0.476 4.281 19028 Z= 0.246 Chirality : 0.042 0.153 2136 Planarity : 0.004 0.033 2392 Dihedral : 6.847 84.601 2092 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.15 % Allowed : 11.17 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1680 helix: 1.77 (0.17), residues: 892 sheet: 0.00 (0.34), residues: 220 loop : -1.54 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.003 0.001 HIS B 141 PHE 0.010 0.001 PHE C 384 TYR 0.011 0.001 TYR C 589 ARG 0.005 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 684) hydrogen bonds : angle 4.37481 ( 2004) covalent geometry : bond 0.00323 (13976) covalent geometry : angle 0.47605 (19028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10135.87 seconds wall clock time: 175 minutes 19.19 seconds (10519.19 seconds total)