Starting phenix.real_space_refine on Fri Aug 9 23:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/08_2024/6lvd_0990.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 17444 2.51 5 N 4836 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "G PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.91, per 1000 atoms: 0.50 Number of scatterers: 27628 At special positions: 0 Unit cell: (120.91, 155.15, 104.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 5252 8.00 N 4836 7.00 C 17444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.74 Conformation dependent library (CDL) restraints added in 4.8 seconds 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 21.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.675A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.656A pdb=" N TYR A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.652A pdb=" N LEU A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.356A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.883A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.633A pdb=" N ALA A 597 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.012A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.831A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.645A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.517A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.277A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 72 through 78 removed outlier: 6.264A pdb=" N THR B 75 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.770A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.698A pdb=" N TYR C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.886A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 488 removed outlier: 4.376A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.127A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.773A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 599 through 605 removed outlier: 3.975A pdb=" N ILE C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 732 removed outlier: 4.341A pdb=" N GLY C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 19 through 41 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.705A pdb=" N TYR E 327 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.920A pdb=" N VAL E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 428 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 488 removed outlier: 3.518A pdb=" N ASP E 478 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.127A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 removed outlier: 3.769A pdb=" N ASP E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 597 Processing helix chain 'E' and resid 599 through 605 removed outlier: 3.971A pdb=" N ILE E 603 " --> pdb=" O ALA E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 19 through 41 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.597A pdb=" N ALA F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 258 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLN G 326 " --> pdb=" O CYS G 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 327 " --> pdb=" O PRO G 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 323 through 327' Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.672A pdb=" N TYR G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 431 Processing helix chain 'G' and resid 432 through 435 Processing helix chain 'G' and resid 458 through 462 removed outlier: 3.566A pdb=" N LEU G 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 458 through 462' Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.676A pdb=" N ALA G 477 " --> pdb=" O TRP G 473 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 3.881A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 536 Processing helix chain 'G' and resid 593 through 597 removed outlier: 3.638A pdb=" N ALA G 597 " --> pdb=" O ARG G 594 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 604 removed outlier: 3.999A pdb=" N ILE G 603 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 691 removed outlier: 3.800A pdb=" N LYS G 691 " --> pdb=" O PRO G 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 688 through 691' Processing helix chain 'G' and resid 726 through 730 removed outlier: 3.807A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 726 through 730' Processing helix chain 'G' and resid 740 through 754 removed outlier: 3.520A pdb=" N ILE G 754 " --> pdb=" O LEU G 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.284A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 72 through 78 removed outlier: 6.258A pdb=" N THR H 75 " --> pdb=" O MET H 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.776A pdb=" N ALA H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.679A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 36 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.345A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 330 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 658 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 611 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 656 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE A 613 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 13.620A pdb=" N GLY A 654 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.579A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.989A pdb=" N SER C 122 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP C 116 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TRP C 124 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER C 114 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 126 " --> pdb=" O ILE C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.796A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 522 through 523 Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.581A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E 38 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 54 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.985A pdb=" N SER E 122 " --> pdb=" O TRP E 116 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP E 116 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TRP E 124 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER E 114 " --> pdb=" O TRP E 124 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU E 126 " --> pdb=" O ILE E 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.471A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.439A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AD4, first strand: chain 'E' and resid 451 through 453 Processing sheet with id=AD5, first strand: chain 'E' and resid 522 through 523 Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.676A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.067A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 360 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 33 through 36 removed outlier: 3.568A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 330 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.543A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 420 through 421 removed outlier: 3.515A pdb=" N TYR H 80 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AE5, first strand: chain 'G' and resid 522 through 523 Processing sheet with id=AE6, first strand: chain 'G' and resid 657 through 660 removed outlier: 6.697A pdb=" N LEU G 658 " --> pdb=" O SER G 609 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2697 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: 12.19 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8905 1.33 - 1.45: 5400 1.45 - 1.57: 13951 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28412 Sorted by residual: bond pdb=" CG1 ILE G 161 " pdb=" CD1 ILE G 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.60e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.57e+00 bond pdb=" C LEU C 461 " pdb=" N ARG C 462 " ideal model delta sigma weight residual 1.329 1.295 0.034 1.60e-02 3.91e+03 4.40e+00 bond pdb=" CG LEU C 330 " pdb=" CD1 LEU C 330 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CG1 ILE G 244 " pdb=" CD1 ILE G 244 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.76e+00 ... (remaining 28407 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.80: 566 104.80 - 112.13: 12977 112.13 - 119.46: 10114 119.46 - 126.79: 14351 126.79 - 134.11: 588 Bond angle restraints: 38596 Sorted by residual: angle pdb=" N GLY C 548 " pdb=" CA GLY C 548 " pdb=" C GLY C 548 " ideal model delta sigma weight residual 112.77 119.46 -6.69 1.28e+00 6.10e-01 2.73e+01 angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C GLY E 655 " pdb=" N TYR E 656 " pdb=" CA TYR E 656 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" CA TYR C 522 " pdb=" CB TYR C 522 " pdb=" CG TYR C 522 " ideal model delta sigma weight residual 113.90 121.43 -7.53 1.80e+00 3.09e-01 1.75e+01 ... (remaining 38591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 15676 15.40 - 30.81: 735 30.81 - 46.21: 110 46.21 - 61.62: 9 61.62 - 77.02: 6 Dihedral angle restraints: 16536 sinusoidal: 6628 harmonic: 9908 Sorted by residual: dihedral pdb=" CA ASN G 547 " pdb=" C ASN G 547 " pdb=" N GLY G 548 " pdb=" CA GLY G 548 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASN E 547 " pdb=" C ASN E 547 " pdb=" N GLY E 548 " pdb=" CA GLY E 548 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY A 579 " pdb=" C GLY A 579 " pdb=" N GLU A 580 " pdb=" CA GLU A 580 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3441 0.092 - 0.184: 446 0.184 - 0.276: 21 0.276 - 0.368: 4 0.368 - 0.460: 4 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CB ILE G 283 " pdb=" CA ILE G 283 " pdb=" CG1 ILE G 283 " pdb=" CG2 ILE G 283 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3913 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.85e+00 pdb=" CG TRP A 331 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 331 " -0.019 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP G 331 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP G 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 331 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 331 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 331 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 331 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 656 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C TYR C 656 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR C 656 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU C 657 " -0.016 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4726 2.76 - 3.29: 23782 3.29 - 3.83: 46353 3.83 - 4.36: 57039 4.36 - 4.90: 99884 Nonbonded interactions: 231784 Sorted by model distance: nonbonded pdb=" O ILE E 552 " pdb=" OH TYR E 583 " model vdw 2.223 3.040 nonbonded pdb=" O ILE C 552 " pdb=" OH TYR C 583 " model vdw 2.227 3.040 nonbonded pdb=" O HIS G 615 " pdb=" OH TYR G 684 " model vdw 2.246 3.040 nonbonded pdb=" O HIS C 615 " pdb=" OH TYR C 684 " model vdw 2.246 3.040 nonbonded pdb=" O HIS A 615 " pdb=" OH TYR A 684 " model vdw 2.248 3.040 ... (remaining 231779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 72.780 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.140 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.009 0.100 28412 Z= 0.621 Angle : 0.925 8.837 38596 Z= 0.519 Chirality : 0.061 0.460 3916 Planarity : 0.008 0.061 5116 Dihedral : 9.355 77.019 10248 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.31 % Allowed : 1.29 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.11), residues: 3424 helix: -2.37 (0.15), residues: 592 sheet: -1.93 (0.19), residues: 652 loop : -2.52 (0.10), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 331 HIS 0.017 0.003 HIS C 582 PHE 0.032 0.004 PHE A 332 TYR 0.045 0.004 TYR G 684 ARG 0.011 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 476 time to evaluate : 3.266 Fit side-chains REVERT: B 51 ASN cc_start: 0.7958 (t0) cc_final: 0.7757 (t0) REVERT: B 112 GLU cc_start: 0.8370 (pt0) cc_final: 0.8041 (pm20) REVERT: C 65 GLN cc_start: 0.8246 (mt0) cc_final: 0.7997 (mt0) REVERT: C 425 ASP cc_start: 0.7864 (m-30) cc_final: 0.7597 (m-30) REVERT: C 474 GLU cc_start: 0.7730 (mp0) cc_final: 0.7472 (mp0) REVERT: C 642 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7881 (mtt180) REVERT: D 31 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7570 (mpp80) REVERT: D 110 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8232 (mmtm) REVERT: E 65 GLN cc_start: 0.8241 (mt0) cc_final: 0.7990 (mt0) REVERT: E 425 ASP cc_start: 0.7826 (m-30) cc_final: 0.7558 (m-30) REVERT: F 31 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7664 (mpp80) REVERT: F 110 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8221 (mmtm) REVERT: H 51 ASN cc_start: 0.8041 (t0) cc_final: 0.7826 (t0) REVERT: H 113 GLU cc_start: 0.8735 (mp0) cc_final: 0.8424 (mp0) outliers start: 9 outliers final: 2 residues processed: 485 average time/residue: 0.4381 time to fit residues: 319.8314 Evaluate side-chains 278 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain G residue 553 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 308 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN C 121 GLN C 171 GLN C 403 GLN C 424 ASN C 699 ASN D 14 ASN E 171 GLN E 322 HIS E 403 GLN E 424 ASN E 519 HIS E 699 ASN G 480 HIS H 68 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28412 Z= 0.179 Angle : 0.558 6.978 38596 Z= 0.304 Chirality : 0.044 0.195 3916 Planarity : 0.005 0.045 5116 Dihedral : 5.439 52.771 3858 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.26 % Allowed : 4.36 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 3424 helix: -0.41 (0.19), residues: 608 sheet: -1.29 (0.21), residues: 568 loop : -2.06 (0.11), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 22 HIS 0.004 0.001 HIS G 480 PHE 0.014 0.002 PHE C 332 TYR 0.018 0.001 TYR E 661 ARG 0.006 0.001 ARG E 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 340 time to evaluate : 3.431 Fit side-chains REVERT: C 425 ASP cc_start: 0.7983 (m-30) cc_final: 0.7629 (m-30) REVERT: D 110 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8260 (mmtm) REVERT: E 425 ASP cc_start: 0.7970 (m-30) cc_final: 0.7600 (m-30) REVERT: E 629 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8354 (mtm180) REVERT: F 37 ILE cc_start: 0.8667 (mt) cc_final: 0.8466 (mp) REVERT: F 80 TYR cc_start: 0.7889 (m-80) cc_final: 0.7636 (m-80) REVERT: F 110 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8289 (mmtm) outliers start: 36 outliers final: 20 residues processed: 361 average time/residue: 0.4459 time to fit residues: 247.6435 Evaluate side-chains 272 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 0.9990 chunk 334 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 403 GLN G 486 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 28412 Z= 0.436 Angle : 0.627 6.303 38596 Z= 0.337 Chirality : 0.048 0.198 3916 Planarity : 0.005 0.049 5116 Dihedral : 5.468 52.398 3858 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.64 % Allowed : 6.21 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3424 helix: 0.44 (0.20), residues: 604 sheet: -1.27 (0.20), residues: 608 loop : -1.89 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 101 HIS 0.010 0.002 HIS C 582 PHE 0.015 0.002 PHE A 611 TYR 0.028 0.002 TYR C 661 ARG 0.006 0.001 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 265 time to evaluate : 2.306 Fit side-chains REVERT: A 1 MET cc_start: 0.8022 (mtm) cc_final: 0.7707 (mtt) REVERT: A 622 MET cc_start: 0.8992 (mmp) cc_final: 0.8500 (mmp) REVERT: C 425 ASP cc_start: 0.8019 (m-30) cc_final: 0.7733 (m-30) REVERT: D 37 ILE cc_start: 0.8633 (mp) cc_final: 0.8362 (mp) REVERT: D 110 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8319 (mmtm) REVERT: E 405 MET cc_start: 0.8103 (ttm) cc_final: 0.7829 (mtp) REVERT: E 425 ASP cc_start: 0.8051 (m-30) cc_final: 0.7678 (m-30) REVERT: F 37 ILE cc_start: 0.8595 (mt) cc_final: 0.8341 (mp) REVERT: F 110 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8327 (mmtm) REVERT: G 622 MET cc_start: 0.9049 (mmp) cc_final: 0.8545 (mmp) outliers start: 47 outliers final: 38 residues processed: 294 average time/residue: 0.3234 time to fit residues: 150.1919 Evaluate side-chains 284 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 VAL Chi-restraints excluded: chain H residue 8 CYS Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: