Starting phenix.real_space_refine on Mon Oct 14 18:02:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b64_44245/10_2024/9b64_44245.cif" } resolution = 3.56 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= 0.002 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 128 5.16 5 C 12029 2.51 5 N 2984 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 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: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 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: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.25 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.75 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.43 Time building chain proxies: 16.07, per 1000 atoms: 0.87 Number of scatterers: 18493 At special positions: 0 Unit cell: (116.44, 110.7, 146.78, 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 128 16.00 O 3352 8.00 N 2984 7.00 C 12029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 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: 4.41 Conformation dependent library (CDL) restraints added in 3.6 seconds 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4366 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 61.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.552A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.783A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.953A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.642A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.875A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.883A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.665A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.907A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.825A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.779A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.800A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.870A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.853A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.800A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 removed outlier: 3.534A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.682A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.890A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.767A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.550A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.844A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 removed outlier: 3.558A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.772A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 489 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.813A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.749A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.784A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 3.560A pdb=" N ILE G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.701A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.720A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AA4, first strand: chain 'C' and resid 406 through 408 Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.564A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.820A pdb=" N LEU C 703 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.520A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.699A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.661A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.665A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.183A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.437A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.608A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.392A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 78 through 79 1216 hydrogen bonds defined for protein. 3526 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: 6.70 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5691 1.34 - 1.46: 4848 1.46 - 1.58: 8161 1.58 - 1.70: 1 1.70 - 1.82: 208 Bond restraints: 18909 Sorted by residual: bond pdb=" CB PRO C 745 " pdb=" CG PRO C 745 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.88e+00 bond pdb=" CG LEU B 751 " pdb=" CD2 LEU B 751 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.42e+00 bond pdb=" CB GLU D 705 " pdb=" CG GLU D 705 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB GLU C 644 " pdb=" CG GLU C 644 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB PRO C 737 " pdb=" CG PRO C 737 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.17e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 25303 2.58 - 5.15: 225 5.15 - 7.73: 21 7.73 - 10.31: 13 10.31 - 12.88: 3 Bond angle restraints: 25565 Sorted by residual: angle pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" CD PRO C 745 " ideal model delta sigma weight residual 112.00 104.26 7.74 1.40e+00 5.10e-01 3.05e+01 angle pdb=" C LYS C 765 " pdb=" N TRP C 766 " pdb=" CA TRP C 766 " ideal model delta sigma weight residual 122.49 114.45 8.04 1.55e+00 4.16e-01 2.69e+01 angle pdb=" CG ARG F 99 " pdb=" CD ARG F 99 " pdb=" NE ARG F 99 " ideal model delta sigma weight residual 112.00 121.95 -9.95 2.20e+00 2.07e-01 2.04e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA GLN E 207 " pdb=" CB GLN E 207 " pdb=" CG GLN E 207 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 ... (remaining 25560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9443 17.86 - 35.72: 1281 35.72 - 53.57: 285 53.57 - 71.43: 33 71.43 - 89.29: 25 Dihedral angle restraints: 11067 sinusoidal: 4227 harmonic: 6840 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 165.14 -72.14 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 157.65 -64.65 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 151.50 -58.50 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 11064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1964 0.036 - 0.072: 693 0.072 - 0.107: 177 0.107 - 0.143: 38 0.143 - 0.179: 5 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" C PRO C 745 " pdb=" CB PRO C 745 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 812 " pdb=" CA ILE A 812 " pdb=" CG1 ILE A 812 " pdb=" CG2 ILE A 812 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TRP C 766 " pdb=" N TRP C 766 " pdb=" C TRP C 766 " pdb=" CB TRP C 766 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2874 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 766 " -0.034 2.00e-02 2.50e+03 3.38e-02 2.86e+01 pdb=" CG TRP C 766 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP C 766 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP C 766 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 766 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 766 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 766 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 766 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 766 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 766 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 671 " -0.039 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP B 671 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 671 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 671 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 671 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 671 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 671 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 671 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 671 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 671 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 403 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 404 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.050 5.00e-02 4.00e+02 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1628 2.74 - 3.28: 19039 3.28 - 3.82: 32205 3.82 - 4.36: 35342 4.36 - 4.90: 62298 Nonbonded interactions: 150512 Sorted by model distance: nonbonded pdb=" N LEU G 3 " pdb=" OE1 GLN G 9 " model vdw 2.201 3.120 nonbonded pdb=" O VAL C 681 " pdb=" OH TYR C 700 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU A 657 " pdb=" NH2 ARG A 660 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN B 642 " pdb=" O ILE B 645 " model vdw 2.261 3.120 ... (remaining 150507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 and (n \ ame N or name CA or name C or name O or name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 through 812 \ or (resid 813 and (name N or name CA or name C or name O or name CB )) or resid \ 814 through 818 or (resid 819 through 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 773 or (resid 784 and (name N or name CA or name C or name O or nam \ e CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.910 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 48.700 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 18909 Z= 0.195 Angle : 0.640 12.884 25565 Z= 0.337 Chirality : 0.039 0.179 2877 Planarity : 0.005 0.102 3155 Dihedral : 16.807 89.291 6665 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 27.72 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.70 (0.18), residues: 2337 helix: 2.44 (0.14), residues: 1393 sheet: -0.74 (0.37), residues: 192 loop : -0.91 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP C 766 HIS 0.007 0.001 HIS H 205 PHE 0.015 0.001 PHE D 658 TYR 0.019 0.001 TYR E 156 ARG 0.010 0.001 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 346 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (mp) REVERT: F 117 MET cc_start: 0.7842 (mmt) cc_final: 0.7639 (mmm) REVERT: F 178 TRP cc_start: 0.7586 (p-90) cc_final: 0.4641 (m100) REVERT: F 204 ARG cc_start: 0.6746 (ptm160) cc_final: 0.6543 (ptm160) REVERT: C 641 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7445 (mttt) REVERT: A 769 ASP cc_start: 0.7559 (m-30) cc_final: 0.7324 (t0) REVERT: D 816 TYR cc_start: 0.7431 (t80) cc_final: 0.7179 (t80) REVERT: E 5 ASP cc_start: 0.5721 (m-30) cc_final: 0.5263 (m-30) REVERT: E 78 LYS cc_start: 0.7427 (ptmt) cc_final: 0.6807 (pttt) outliers start: 3 outliers final: 2 residues processed: 348 average time/residue: 0.3282 time to fit residues: 172.0967 Evaluate side-chains 330 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 327 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN F 149 ASN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18909 Z= 0.151 Angle : 0.520 10.054 25565 Z= 0.267 Chirality : 0.039 0.179 2877 Planarity : 0.004 0.083 3155 Dihedral : 3.748 57.443 2568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.31 % Allowed : 25.00 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 2.21 (0.18), residues: 2337 helix: 2.87 (0.14), residues: 1403 sheet: -0.51 (0.38), residues: 180 loop : -0.86 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP C 766 HIS 0.006 0.001 HIS E 82 PHE 0.012 0.001 PHE C 814 TYR 0.014 0.001 TYR B 673 ARG 0.008 0.001 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 367 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8550 (mp) REVERT: H 200 MET cc_start: 0.8006 (mmm) cc_final: 0.7801 (mmp) REVERT: F 99 ARG cc_start: 0.6613 (ptm160) cc_final: 0.5911 (ptm160) REVERT: F 126 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5991 (tm-30) REVERT: C 502 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 641 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7365 (mttt) REVERT: C 714 GLN cc_start: 0.8448 (mm110) cc_final: 0.8242 (mm-40) REVERT: A 769 ASP cc_start: 0.7576 (m-30) cc_final: 0.7345 (t0) REVERT: A 789 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9038 (tt) REVERT: D 816 TYR cc_start: 0.7402 (t80) cc_final: 0.7142 (t80) REVERT: E 5 ASP cc_start: 0.5658 (m-30) cc_final: 0.5229 (m-30) REVERT: E 6 ARG cc_start: 0.6102 (mmm-85) cc_final: 0.5521 (mmt180) REVERT: E 33 TRP cc_start: 0.8899 (m100) cc_final: 0.8645 (m100) REVERT: E 58 MET cc_start: 0.7258 (mtp) cc_final: 0.6784 (mtp) REVERT: E 78 LYS cc_start: 0.7282 (ptmt) cc_final: 0.6605 (pttt) REVERT: E 200 MET cc_start: 0.7338 (ptp) cc_final: 0.7082 (ptp) outliers start: 45 outliers final: 21 residues processed: 395 average time/residue: 0.3122 time to fit residues: 187.0311 Evaluate side-chains 357 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 333 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8606 > 50: distance: 17 - 158: 5.475 distance: 30 - 144: 3.729 distance: 33 - 141: 11.619 distance: 113 - 114: 6.070 distance: 113 - 119: 3.255 distance: 114 - 115: 12.399 distance: 114 - 117: 9.319 distance: 115 - 116: 9.895 distance: 115 - 120: 7.423 distance: 117 - 118: 10.746 distance: 118 - 119: 4.055 distance: 120 - 121: 17.134 distance: 121 - 122: 14.322 distance: 121 - 124: 11.760 distance: 122 - 123: 22.206 distance: 122 - 126: 17.290 distance: 124 - 125: 7.161 distance: 125 - 196: 6.866 distance: 126 - 127: 8.126 distance: 127 - 128: 7.510 distance: 127 - 130: 18.727 distance: 128 - 134: 3.261 distance: 130 - 131: 9.109 distance: 131 - 132: 17.902 distance: 131 - 133: 18.437 distance: 134 - 135: 6.985 distance: 135 - 136: 9.775 distance: 136 - 137: 9.891 distance: 136 - 141: 10.604 distance: 138 - 139: 8.976 distance: 138 - 140: 10.053 distance: 141 - 142: 8.199 distance: 142 - 143: 5.342 distance: 142 - 145: 4.400 distance: 143 - 144: 3.225 distance: 143 - 149: 5.931 distance: 145 - 146: 9.422 distance: 146 - 147: 3.895 distance: 147 - 148: 4.478 distance: 150 - 151: 3.692 distance: 150 - 153: 8.632 distance: 151 - 152: 5.815 distance: 151 - 158: 6.448 distance: 153 - 154: 5.854 distance: 154 - 155: 8.457 distance: 155 - 156: 9.538 distance: 156 - 157: 11.916 distance: 158 - 159: 4.627 distance: 159 - 160: 5.356 distance: 160 - 165: 3.586 distance: 162 - 163: 7.811 distance: 162 - 164: 8.034 distance: 165 - 166: 9.645 distance: 166 - 167: 8.299 distance: 167 - 168: 4.491 distance: 167 - 169: 8.979 distance: 169 - 170: 6.774 distance: 170 - 171: 11.615 distance: 171 - 173: 3.426 distance: 173 - 174: 4.706 distance: 174 - 175: 5.256 distance: 174 - 177: 4.518 distance: 175 - 181: 5.052 distance: 177 - 178: 3.954 distance: 178 - 180: 7.115