Starting phenix.real_space_refine on Wed Jan 22 11:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_44245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_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/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_44245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_44245.map" model { file = "/net/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_44245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b64_44245/01_2025/9b64_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-5571/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: 15.86, per 1000 atoms: 0.86 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: 4.82 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: 2.10 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: 6.16 Time building geometry restraints manager: 5.73 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 48.740 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 2.223 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: 0.3360 time to fit residues: 175.3279 Evaluate side-chains 330 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096379 restraints weight = 89947.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100871 restraints weight = 32567.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103689 restraints weight = 18782.880| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8537 (mp) REVERT: H 200 MET cc_start: 0.8016 (mmm) cc_final: 0.7807 (mmp) REVERT: F 99 ARG cc_start: 0.6609 (ptm160) cc_final: 0.5908 (ptm160) REVERT: F 126 GLU cc_start: 0.6513 (mt-10) cc_final: 0.5986 (tm-30) REVERT: C 502 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (tp) REVERT: C 641 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7364 (mttt) REVERT: C 714 GLN cc_start: 0.8430 (mm110) cc_final: 0.8228 (mm-40) REVERT: A 789 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9041 (tt) REVERT: D 816 TYR cc_start: 0.7419 (t80) cc_final: 0.7154 (t80) REVERT: E 5 ASP cc_start: 0.5686 (m-30) cc_final: 0.5235 (m-30) REVERT: E 6 ARG cc_start: 0.6066 (mmm-85) cc_final: 0.5513 (mmt180) REVERT: E 33 TRP cc_start: 0.8856 (m100) cc_final: 0.8624 (m100) REVERT: E 58 MET cc_start: 0.7228 (mtp) cc_final: 0.6758 (mtp) REVERT: E 78 LYS cc_start: 0.7287 (ptmt) cc_final: 0.6613 (pttt) REVERT: E 200 MET cc_start: 0.7268 (ptp) cc_final: 0.7027 (ptp) outliers start: 45 outliers final: 21 residues processed: 395 average time/residue: 0.3495 time to fit residues: 208.9791 Evaluate side-chains 359 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 134 optimal weight: 0.0670 chunk 224 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS B 756 GLN D 508 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 207 GLN G 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092602 restraints weight = 105715.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097728 restraints weight = 34281.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099201 restraints weight = 16909.971| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18909 Z= 0.261 Angle : 0.566 8.368 25565 Z= 0.294 Chirality : 0.041 0.170 2877 Planarity : 0.004 0.070 3155 Dihedral : 3.754 51.128 2565 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.59 % Allowed : 24.54 % Favored : 71.87 % 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: 2.03 (0.18), residues: 2337 helix: 2.66 (0.14), residues: 1403 sheet: -0.48 (0.39), residues: 166 loop : -0.78 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP C 766 HIS 0.004 0.001 HIS F 60 PHE 0.015 0.001 PHE B 659 TYR 0.023 0.002 TYR B 673 ARG 0.009 0.001 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 3 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 423 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.0200 (OUTLIER) cc_final: -0.0418 (t70) REVERT: H 117 MET cc_start: 0.7782 (mmm) cc_final: 0.7456 (mtp) REVERT: H 199 HIS cc_start: 0.7918 (t70) cc_final: 0.7618 (t70) REVERT: F 99 ARG cc_start: 0.6507 (ptm160) cc_final: 0.6137 (ptm160) REVERT: F 126 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6275 (tm-30) REVERT: C 407 MET cc_start: 0.7010 (ptp) cc_final: 0.6598 (ptm) REVERT: C 641 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7412 (mttt) REVERT: C 814 PHE cc_start: 0.7948 (t80) cc_final: 0.7694 (t80) REVERT: B 634 GLU cc_start: 0.7259 (tp30) cc_final: 0.6880 (tp30) REVERT: B 702 TYR cc_start: 0.8184 (t80) cc_final: 0.7743 (t80) REVERT: A 634 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7236 (pt0) REVERT: D 463 MET cc_start: 0.8287 (mmt) cc_final: 0.7073 (mmt) REVERT: D 629 MET cc_start: 0.7770 (mmm) cc_final: 0.7550 (mmt) REVERT: D 816 TYR cc_start: 0.7480 (t80) cc_final: 0.7247 (t80) REVERT: E 31 ASP cc_start: 0.7441 (p0) cc_final: 0.7220 (t70) outliers start: 70 outliers final: 46 residues processed: 398 average time/residue: 0.3541 time to fit residues: 212.3867 Evaluate side-chains 367 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 721 MET 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 660 ARG Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 121 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 175 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.0000 chunk 139 optimal weight: 10.0000 chunk 148 optimal weight: 0.0040 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094103 restraints weight = 87786.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098547 restraints weight = 31235.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101286 restraints weight = 17931.335| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18909 Z= 0.171 Angle : 0.523 11.787 25565 Z= 0.267 Chirality : 0.039 0.176 2877 Planarity : 0.004 0.063 3155 Dihedral : 3.485 22.656 2563 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.72 % Allowed : 25.46 % Favored : 71.82 % 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: 2.17 (0.18), residues: 2337 helix: 2.79 (0.14), residues: 1403 sheet: -0.54 (0.38), residues: 166 loop : -0.74 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 766 HIS 0.004 0.001 HIS H 205 PHE 0.013 0.001 PHE A 814 TYR 0.018 0.001 TYR E 156 ARG 0.006 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 4 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 405 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 352 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.0175 (OUTLIER) cc_final: -0.0490 (t70) REVERT: H 115 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8461 (mp) REVERT: H 199 HIS cc_start: 0.7789 (t70) cc_final: 0.7520 (t70) REVERT: F 31 ASP cc_start: 0.7816 (m-30) cc_final: 0.7412 (p0) REVERT: F 99 ARG cc_start: 0.6465 (ptm160) cc_final: 0.5831 (ptm160) REVERT: F 110 LEU cc_start: 0.8017 (tt) cc_final: 0.7772 (tt) REVERT: F 126 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6272 (tm-30) REVERT: C 407 MET cc_start: 0.7132 (ptp) cc_final: 0.6797 (ptm) REVERT: C 641 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7394 (mttt) REVERT: C 814 PHE cc_start: 0.7957 (t80) cc_final: 0.7710 (t80) REVERT: B 439 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7444 (mttp) REVERT: B 486 GLU cc_start: 0.8088 (tp30) cc_final: 0.7755 (tp30) REVERT: B 634 GLU cc_start: 0.7136 (tp30) cc_final: 0.6850 (tp30) REVERT: B 702 TYR cc_start: 0.8208 (t80) cc_final: 0.7827 (t80) REVERT: A 634 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7348 (pt0) REVERT: D 463 MET cc_start: 0.8286 (mmt) cc_final: 0.7059 (mmt) REVERT: D 816 TYR cc_start: 0.7511 (t80) cc_final: 0.7289 (t80) REVERT: E 33 TRP cc_start: 0.8889 (m100) cc_final: 0.8580 (m100) REVERT: E 58 MET cc_start: 0.7226 (mtp) cc_final: 0.6820 (mtp) REVERT: G 70 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.5345 (tp30) outliers start: 53 outliers final: 37 residues processed: 389 average time/residue: 0.3210 time to fit residues: 190.8975 Evaluate side-chains 367 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU 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 589 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095306 restraints weight = 86224.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099821 restraints weight = 30836.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102624 restraints weight = 17756.411| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18909 Z= 0.205 Angle : 0.526 9.896 25565 Z= 0.272 Chirality : 0.039 0.175 2877 Planarity : 0.004 0.059 3155 Dihedral : 3.512 22.108 2563 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.18 % Allowed : 25.10 % Favored : 71.71 % 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: 2.11 (0.18), residues: 2337 helix: 2.75 (0.14), residues: 1403 sheet: -0.63 (0.37), residues: 180 loop : -0.75 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 671 HIS 0.005 0.001 HIS D 412 PHE 0.014 0.001 PHE A 814 TYR 0.017 0.001 TYR E 156 ARG 0.006 0.001 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 5 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 403 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 341 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6748 (p) cc_final: 0.6242 (p) REVERT: H 12 LEU cc_start: 0.8144 (mp) cc_final: 0.7798 (mp) REVERT: H 86 ASP cc_start: 0.0307 (OUTLIER) cc_final: -0.0363 (t70) REVERT: H 115 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8415 (mp) REVERT: H 199 HIS cc_start: 0.7768 (t70) cc_final: 0.7434 (t70) REVERT: H 204 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6426 (ttp80) REVERT: F 31 ASP cc_start: 0.7774 (m-30) cc_final: 0.7548 (p0) REVERT: F 76 LEU cc_start: 0.6545 (mp) cc_final: 0.6053 (mm) REVERT: F 126 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6291 (tm-30) REVERT: C 407 MET cc_start: 0.7027 (ptp) cc_final: 0.6724 (ptm) REVERT: C 641 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7398 (mttt) REVERT: C 814 PHE cc_start: 0.7956 (t80) cc_final: 0.7673 (t80) REVERT: B 702 TYR cc_start: 0.8230 (t80) cc_final: 0.7855 (t80) REVERT: A 634 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7328 (pt0) REVERT: D 463 MET cc_start: 0.8284 (mmt) cc_final: 0.7106 (mmt) REVERT: D 816 TYR cc_start: 0.7534 (t80) cc_final: 0.7318 (t80) REVERT: E 33 TRP cc_start: 0.8864 (m100) cc_final: 0.8546 (m100) REVERT: G 70 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5401 (tp30) outliers start: 62 outliers final: 50 residues processed: 385 average time/residue: 0.3400 time to fit residues: 199.8100 Evaluate side-chains 373 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 744 THR 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 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 160 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097297 restraints weight = 94162.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102012 restraints weight = 32030.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104936 restraints weight = 17989.028| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18909 Z= 0.144 Angle : 0.513 11.453 25565 Z= 0.261 Chirality : 0.039 0.163 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.379 20.556 2563 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.93 % Allowed : 25.82 % Favored : 71.25 % 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: 2.31 (0.18), residues: 2337 helix: 2.93 (0.13), residues: 1399 sheet: -0.41 (0.39), residues: 166 loop : -0.74 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 671 HIS 0.005 0.001 HIS H 205 PHE 0.025 0.001 PHE D 546 TYR 0.018 0.001 TYR E 156 ARG 0.007 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 6 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 to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6601 (p) cc_final: 0.6102 (p) REVERT: H 12 LEU cc_start: 0.8115 (mp) cc_final: 0.7779 (mp) REVERT: H 86 ASP cc_start: 0.0074 (OUTLIER) cc_final: -0.0593 (t0) REVERT: H 127 PHE cc_start: 0.5471 (OUTLIER) cc_final: 0.5177 (m-10) REVERT: H 131 ARG cc_start: 0.4975 (mmp-170) cc_final: 0.4756 (mmm160) REVERT: H 199 HIS cc_start: 0.7724 (t70) cc_final: 0.7426 (t70) REVERT: H 204 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.6423 (ttp80) REVERT: F 76 LEU cc_start: 0.6180 (mp) cc_final: 0.5753 (mm) REVERT: F 86 ASP cc_start: 0.1455 (OUTLIER) cc_final: 0.1173 (t70) REVERT: F 99 ARG cc_start: 0.6299 (ptm160) cc_final: 0.5606 (ptm160) REVERT: F 126 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6264 (tm-30) REVERT: C 407 MET cc_start: 0.6867 (ptp) cc_final: 0.6613 (ptm) REVERT: C 441 LYS cc_start: 0.8362 (tmtt) cc_final: 0.7957 (mmmt) REVERT: C 641 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7396 (mttt) REVERT: C 814 PHE cc_start: 0.7986 (t80) cc_final: 0.7668 (t80) REVERT: B 702 TYR cc_start: 0.8211 (t80) cc_final: 0.7847 (t80) REVERT: B 755 GLU cc_start: 0.8410 (mp0) cc_final: 0.8100 (mp0) REVERT: A 399 THR cc_start: 0.8831 (p) cc_final: 0.8503 (m) REVERT: A 634 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7379 (pt0) REVERT: D 463 MET cc_start: 0.8203 (mmt) cc_final: 0.7149 (mmt) REVERT: D 816 TYR cc_start: 0.7492 (t80) cc_final: 0.7283 (t80) REVERT: E 33 TRP cc_start: 0.8835 (m100) cc_final: 0.8542 (m100) REVERT: G 37 ARG cc_start: 0.5298 (ptt-90) cc_final: 0.4631 (ptt-90) REVERT: G 70 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5382 (tp30) REVERT: G 98 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7367 (mp) outliers start: 57 outliers final: 39 residues processed: 395 average time/residue: 0.3255 time to fit residues: 194.2206 Evaluate side-chains 368 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 324 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR 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 629 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 125 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096471 restraints weight = 102772.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102188 restraints weight = 36687.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104487 restraints weight = 16910.336| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18909 Z= 0.167 Angle : 0.520 11.542 25565 Z= 0.267 Chirality : 0.039 0.166 2877 Planarity : 0.004 0.053 3155 Dihedral : 3.388 26.030 2563 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.18 % Allowed : 25.82 % Favored : 71.00 % 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: 2.31 (0.18), residues: 2337 helix: 2.92 (0.13), residues: 1399 sheet: -0.42 (0.39), residues: 166 loop : -0.73 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP B 671 HIS 0.005 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.018 0.001 TYR E 156 ARG 0.008 0.001 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 7 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 393 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6616 (p) cc_final: 0.6150 (p) REVERT: H 12 LEU cc_start: 0.8032 (mp) cc_final: 0.7699 (mp) REVERT: H 86 ASP cc_start: 0.0222 (OUTLIER) cc_final: -0.0434 (t0) REVERT: H 127 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5258 (m-10) REVERT: H 204 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6517 (mtm110) REVERT: F 76 LEU cc_start: 0.6173 (mp) cc_final: 0.5836 (mm) REVERT: F 86 ASP cc_start: 0.1585 (OUTLIER) cc_final: 0.1232 (t70) REVERT: F 99 ARG cc_start: 0.6300 (ptm160) cc_final: 0.5655 (ptm160) REVERT: F 102 ARG cc_start: 0.6463 (tpt90) cc_final: 0.6131 (tpt170) REVERT: F 126 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6335 (tm-30) REVERT: F 185 LEU cc_start: 0.8738 (mt) cc_final: 0.8419 (mp) REVERT: C 407 MET cc_start: 0.6986 (ptp) cc_final: 0.6642 (ptm) REVERT: C 441 LYS cc_start: 0.8339 (tmtt) cc_final: 0.7871 (mmmt) REVERT: C 641 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7454 (mttt) REVERT: C 642 GLN cc_start: 0.6304 (pp30) cc_final: 0.5603 (tm-30) REVERT: C 814 PHE cc_start: 0.7987 (t80) cc_final: 0.7711 (t80) REVERT: B 702 TYR cc_start: 0.8260 (t80) cc_final: 0.7914 (t80) REVERT: B 755 GLU cc_start: 0.8387 (mp0) cc_final: 0.8045 (mp0) REVERT: A 399 THR cc_start: 0.8820 (p) cc_final: 0.8516 (m) REVERT: A 634 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7389 (pt0) REVERT: A 660 ARG cc_start: 0.6234 (ttm-80) cc_final: 0.5899 (mtm-85) REVERT: D 633 ILE cc_start: 0.8779 (mm) cc_final: 0.8573 (tp) REVERT: G 10 MET cc_start: 0.7639 (tpp) cc_final: 0.7018 (tpp) REVERT: G 70 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5505 (tp30) outliers start: 62 outliers final: 46 residues processed: 377 average time/residue: 0.3311 time to fit residues: 188.0324 Evaluate side-chains 373 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 736 THR 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 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6973 > 50: distance: 88 - 105: 15.209 distance: 92 - 113: 17.315 distance: 97 - 121: 6.492 distance: 100 - 105: 16.042 distance: 101 - 126: 9.071 distance: 105 - 106: 31.372 distance: 106 - 107: 12.083 distance: 106 - 109: 8.605 distance: 107 - 108: 20.394 distance: 107 - 113: 19.951 distance: 108 - 133: 30.619 distance: 109 - 110: 9.792 distance: 110 - 111: 14.090 distance: 110 - 112: 19.377 distance: 113 - 114: 16.845 distance: 114 - 115: 11.965 distance: 114 - 117: 16.397 distance: 115 - 116: 8.828 distance: 115 - 121: 12.493 distance: 116 - 141: 13.974 distance: 117 - 118: 11.840 distance: 118 - 119: 9.689 distance: 118 - 120: 21.431 distance: 121 - 122: 6.610 distance: 122 - 123: 12.620 distance: 122 - 125: 18.106 distance: 123 - 124: 16.558 distance: 123 - 126: 11.233 distance: 124 - 150: 9.000 distance: 126 - 127: 9.059 distance: 127 - 128: 6.901 distance: 127 - 130: 8.186 distance: 128 - 129: 20.465 distance: 128 - 133: 13.328 distance: 129 - 158: 16.704 distance: 130 - 131: 15.248 distance: 130 - 132: 10.182 distance: 133 - 134: 9.450 distance: 134 - 135: 6.387 distance: 134 - 137: 13.312 distance: 135 - 136: 6.318 distance: 135 - 141: 13.142 distance: 136 - 164: 23.530 distance: 137 - 138: 24.079 distance: 138 - 139: 12.039 distance: 138 - 140: 18.894 distance: 141 - 142: 9.563 distance: 142 - 143: 8.608 distance: 142 - 145: 6.110 distance: 143 - 144: 7.453 distance: 143 - 150: 13.352 distance: 144 - 173: 14.202 distance: 145 - 146: 6.654 distance: 146 - 147: 6.175 distance: 147 - 148: 16.012 distance: 148 - 149: 14.803 distance: 150 - 151: 10.830 distance: 151 - 152: 7.564 distance: 151 - 154: 12.436 distance: 152 - 153: 5.283 distance: 152 - 158: 14.792 distance: 153 - 182: 22.035 distance: 154 - 155: 15.472 distance: 155 - 156: 19.340 distance: 155 - 157: 9.589 distance: 158 - 159: 17.633 distance: 159 - 160: 22.466 distance: 159 - 162: 30.215 distance: 160 - 161: 15.039 distance: 160 - 164: 8.365 distance: 162 - 163: 7.251 distance: 164 - 165: 7.393 distance: 165 - 166: 17.476 distance: 165 - 168: 17.082 distance: 166 - 167: 13.383 distance: 166 - 173: 16.795 distance: 168 - 169: 17.769 distance: 169 - 170: 7.375 distance: 170 - 171: 8.049 distance: 170 - 172: 14.853 distance: 173 - 174: 10.128 distance: 174 - 175: 22.891 distance: 174 - 177: 8.321 distance: 175 - 176: 15.173 distance: 175 - 182: 19.767 distance: 177 - 178: 11.352 distance: 178 - 179: 12.530 distance: 179 - 180: 3.420 distance: 179 - 181: 9.864