Starting phenix.real_space_refine on Fri Mar 6 00:23:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_29172_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_29172_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_29172_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_29172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhw_29172/03_2026/8fhw_29172.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.181 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5} 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: {'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5} 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: {'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5} 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: {'ARG:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5} 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: 4.45, per 1000 atoms: 0.17 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: 3.91 Conformation dependent library (CDL) restraints added in 877.0 milliseconds 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: 0.73 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: 6.38 Time building geometry restraints manager: 3.21 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.210 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: 0.160 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (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 ARG 0.006 0.001 ARG C 323 TYR 0.010 0.002 TYR D 589 PHE 0.013 0.002 PHE D 310 TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00582 (13976) covalent geometry : angle 0.64135 (19028) hydrogen bonds : bond 0.17354 ( 684) hydrogen bonds : angle 6.15492 ( 2004) *********************** 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 : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3026 time to fit residues: 43.6910 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 : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS C 141 HIS D 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106534 restraints weight = 57861.662| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.39 r_work: 0.3316 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13976 Z= 0.195 Angle : 0.541 4.846 19028 Z= 0.286 Chirality : 0.044 0.155 2136 Planarity : 0.004 0.034 2392 Dihedral : 7.394 88.079 2092 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.64 % Favored : 95.12 % Rotamer: Outliers : 0.29 % Allowed : 7.38 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1680 helix: 0.92 (0.17), residues: 884 sheet: 0.24 (0.35), residues: 220 loop : -1.76 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.015 0.002 TYR A 589 PHE 0.012 0.002 PHE B 100 TRP 0.008 0.001 TRP B 168 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00465 (13976) covalent geometry : angle 0.54097 (19028) hydrogen bonds : bond 0.05390 ( 684) hydrogen bonds : angle 4.94689 ( 2004) *********************** 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 84 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.8759 (tpt) cc_final: 0.8483 (tpt) REVERT: C 534 MET cc_start: 0.8759 (tpt) cc_final: 0.8483 (tpt) REVERT: D 534 MET cc_start: 0.8761 (tpt) cc_final: 0.8485 (tpt) outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 0.2179 time to fit residues: 27.8518 Evaluate side-chains 74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113133 restraints weight = 55271.996| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.23 r_work: 0.3446 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13976 Z= 0.155 Angle : 0.496 4.524 19028 Z= 0.259 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.033 2392 Dihedral : 7.082 87.625 2092 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.21 % Allowed : 9.38 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1680 helix: 1.21 (0.17), residues: 888 sheet: 0.21 (0.34), residues: 220 loop : -1.66 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.013 0.001 TYR D 589 PHE 0.010 0.001 PHE A 310 TRP 0.008 0.001 TRP D 168 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00370 (13976) covalent geometry : angle 0.49563 (19028) hydrogen bonds : bond 0.04693 ( 684) hydrogen bonds : angle 4.68858 ( 2004) *********************** 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 79 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.695 Fit side-chains REVERT: A 534 MET cc_start: 0.8714 (tpt) cc_final: 0.8473 (tpt) REVERT: D 534 MET cc_start: 0.8721 (tpt) cc_final: 0.8482 (tpt) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.2659 time to fit residues: 30.3544 Evaluate side-chains 74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.122848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111719 restraints weight = 55723.740| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.28 r_work: 0.3384 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13976 Z= 0.261 Angle : 0.572 5.058 19028 Z= 0.300 Chirality : 0.045 0.155 2136 Planarity : 0.005 0.036 2392 Dihedral : 7.286 85.375 2092 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.29 % Allowed : 9.96 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1680 helix: 0.91 (0.17), residues: 888 sheet: 0.14 (0.34), residues: 220 loop : -1.81 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 177 TYR 0.016 0.002 TYR C 589 PHE 0.015 0.002 PHE C 100 TRP 0.009 0.002 TRP B 168 HIS 0.003 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00638 (13976) covalent geometry : angle 0.57160 (19028) hydrogen bonds : bond 0.05375 ( 684) hydrogen bonds : angle 4.83075 ( 2004) *********************** 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 96 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 351 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8427 (t) REVERT: B 351 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (t) REVERT: C 351 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8428 (t) REVERT: D 351 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8433 (t) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.2050 time to fit residues: 29.9506 Evaluate side-chains 91 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 590 THR Chi-restraints excluded: chain B residue 141 HIS 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 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 590 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 590 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS C 141 HIS D 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115129 restraints weight = 54731.219| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.27 r_work: 0.3438 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13976 Z= 0.116 Angle : 0.467 4.608 19028 Z= 0.243 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.034 2392 Dihedral : 6.876 86.410 2092 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.15 % Allowed : 10.67 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1680 helix: 1.46 (0.17), residues: 892 sheet: 0.15 (0.34), residues: 220 loop : -1.62 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 177 TYR 0.010 0.001 TYR D 589 PHE 0.009 0.001 PHE B 310 TRP 0.008 0.001 TRP C 168 HIS 0.003 0.000 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00268 (13976) covalent geometry : angle 0.46651 (19028) hydrogen bonds : bond 0.04115 ( 684) hydrogen bonds : angle 4.49865 ( 2004) *********************** 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 93 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.758 Fit side-chains REVERT: A 351 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8419 (t) REVERT: C 351 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8424 (t) REVERT: D 351 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8424 (t) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.2067 time to fit residues: 29.6089 Evaluate side-chains 88 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 590 THR 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 206 LEU 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 153 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113795 restraints weight = 55169.030| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.27 r_work: 0.3424 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13976 Z= 0.153 Angle : 0.485 4.411 19028 Z= 0.253 Chirality : 0.042 0.153 2136 Planarity : 0.004 0.033 2392 Dihedral : 6.852 85.484 2092 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.43 % Allowed : 10.60 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1680 helix: 1.59 (0.17), residues: 888 sheet: 0.09 (0.34), residues: 220 loop : -1.64 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 177 TYR 0.012 0.001 TYR D 589 PHE 0.010 0.002 PHE D 384 TRP 0.008 0.001 TRP C 168 HIS 0.002 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00368 (13976) covalent geometry : angle 0.48526 (19028) hydrogen bonds : bond 0.04371 ( 684) hydrogen bonds : angle 4.51565 ( 2004) *********************** 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 99 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8380 (t) REVERT: B 351 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8391 (t) REVERT: C 351 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (t) REVERT: D 351 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8383 (t) outliers start: 20 outliers final: 12 residues processed: 95 average time/residue: 0.1995 time to fit residues: 30.7469 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 : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 HIS 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 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 206 LEU 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 2 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.125486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114377 restraints weight = 54736.144| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.26 r_work: 0.3428 rms_B_bonded: 1.51 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: 0.8411 moved from start: 0.1522 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= 0.136 Angle : 0.469 4.379 19028 Z= 0.244 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.033 2392 Dihedral : 6.749 84.577 2092 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.07 % Allowed : 11.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1680 helix: 1.75 (0.17), residues: 892 sheet: 0.12 (0.34), residues: 220 loop : -1.60 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 177 TYR 0.011 0.001 TYR C 589 PHE 0.009 0.001 PHE A 384 TRP 0.008 0.001 TRP D 168 HIS 0.002 0.000 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00323 (13976) covalent geometry : angle 0.46947 (19028) hydrogen bonds : bond 0.04137 ( 684) hydrogen bonds : angle 4.42543 ( 2004) *********************** 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 95 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.747 Fit side-chains REVERT: A 351 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8428 (t) REVERT: B 351 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8372 (t) REVERT: C 351 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8431 (t) REVERT: D 351 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8364 (t) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.1921 time to fit residues: 29.2601 Evaluate side-chains 95 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 141 HIS 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 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 206 LEU 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 10 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.126117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115158 restraints weight = 54752.534| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.22 r_work: 0.3444 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1600 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= 0.121 Angle : 0.457 4.262 19028 Z= 0.237 Chirality : 0.041 0.152 2136 Planarity : 0.004 0.032 2392 Dihedral : 6.655 85.505 2092 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.15 % Allowed : 10.96 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1680 helix: 1.90 (0.17), residues: 896 sheet: 0.11 (0.34), residues: 220 loop : -1.54 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 177 TYR 0.010 0.001 TYR C 589 PHE 0.009 0.001 PHE A 384 TRP 0.008 0.001 TRP C 168 HIS 0.002 0.000 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00286 (13976) covalent geometry : angle 0.45706 (19028) hydrogen bonds : bond 0.03953 ( 684) hydrogen bonds : angle 4.33104 ( 2004) *********************** 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 96 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.708 Fit side-chains REVERT: A 351 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 351 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8354 (t) REVERT: C 351 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (t) REVERT: D 351 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8414 (t) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.2060 time to fit residues: 31.5340 Evaluate side-chains 96 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 141 HIS 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 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 206 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112912 restraints weight = 55295.626| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.26 r_work: 0.3417 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1534 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= 0.196 Angle : 0.510 4.651 19028 Z= 0.266 Chirality : 0.043 0.151 2136 Planarity : 0.004 0.032 2392 Dihedral : 6.844 83.762 2092 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.00 % Allowed : 11.17 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1680 helix: 1.67 (0.17), residues: 888 sheet: 0.06 (0.34), residues: 220 loop : -1.65 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 177 TYR 0.013 0.001 TYR D 589 PHE 0.011 0.002 PHE A 100 TRP 0.008 0.001 TRP A 168 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00476 (13976) covalent geometry : angle 0.51036 (19028) hydrogen bonds : bond 0.04604 ( 684) hydrogen bonds : angle 4.48576 ( 2004) *********************** 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 99 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8410 (t) REVERT: B 351 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 351 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8409 (t) REVERT: D 351 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (t) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.1969 time to fit residues: 32.6529 Evaluate side-chains 98 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 351 THR 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 124 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114333 restraints weight = 54729.727| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.26 r_work: 0.3425 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1594 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= 0.133 Angle : 0.470 4.445 19028 Z= 0.244 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.032 2392 Dihedral : 6.750 84.136 2092 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.93 % Allowed : 11.25 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1680 helix: 1.86 (0.17), residues: 892 sheet: 0.12 (0.35), residues: 220 loop : -1.55 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 177 TYR 0.011 0.001 TYR C 589 PHE 0.009 0.001 PHE A 310 TRP 0.008 0.001 TRP C 168 HIS 0.002 0.000 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00317 (13976) covalent geometry : angle 0.47034 (19028) hydrogen bonds : bond 0.04113 ( 684) hydrogen bonds : angle 4.35359 ( 2004) ********************** 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 93 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.724 Fit side-chains REVERT: A 351 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8366 (t) REVERT: B 351 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8360 (t) REVERT: C 351 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8367 (t) REVERT: D 351 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8368 (t) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1983 time to fit residues: 30.7821 Evaluate side-chains 93 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.124936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113809 restraints weight = 54831.602| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.26 r_work: 0.3425 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13976 Z= 0.149 Angle : 0.480 4.322 19028 Z= 0.249 Chirality : 0.042 0.152 2136 Planarity : 0.004 0.032 2392 Dihedral : 6.773 83.459 2092 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.29 % Allowed : 10.89 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1680 helix: 1.84 (0.17), residues: 892 sheet: 0.13 (0.35), residues: 220 loop : -1.56 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 177 TYR 0.011 0.001 TYR C 589 PHE 0.009 0.001 PHE C 384 TRP 0.010 0.001 TRP B 168 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00358 (13976) covalent geometry : angle 0.47975 (19028) hydrogen bonds : bond 0.04235 ( 684) hydrogen bonds : angle 4.37192 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4581.03 seconds wall clock time: 78 minutes 32.30 seconds (4712.30 seconds total)