Starting phenix.real_space_refine on Mon Jun 16 09:41:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b64_44245/06_2025/9b64_44245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b64_44245/06_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_44245/06_2025/9b64_44245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b64_44245/06_2025/9b64_44245.map" model { file = "/net/cci-nas-00/data/ceres_data/9b64_44245/06_2025/9b64_44245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b64_44245/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.25 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.75 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.43 Time building chain proxies: 16.25, per 1000 atoms: 0.88 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: 4.64 Conformation dependent library (CDL) restraints added in 4.1 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: 2.55 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: 6.58 Time building geometry restraints manager: 5.61 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 52.750 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.990 ------------------------------------------------------------------------------- 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 18921 Z= 0.136 Angle : 0.642 12.884 25589 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 Details of bonding type rmsd hydrogen bonds : bond 0.12805 ( 1211) hydrogen bonds : angle 4.92658 ( 3526) SS BOND : bond 0.00430 ( 12) SS BOND : angle 1.64815 ( 24) covalent geometry : bond 0.00299 (18909) covalent geometry : angle 0.64008 (25565) *********************** 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 : 2.090 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: 0.3212 time to fit residues: 167.5789 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 : 2.016 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096383 restraints weight = 89947.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100868 restraints weight = 32564.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103684 restraints weight = 18780.367| |-----------------------------------------------------------------------------| 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 18921 Z= 0.107 Angle : 0.521 10.054 25589 Z= 0.268 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 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1211) hydrogen bonds : angle 3.70331 ( 3526) SS BOND : bond 0.00294 ( 12) SS BOND : angle 0.79508 ( 24) covalent geometry : bond 0.00232 (18909) covalent geometry : angle 0.52023 (25565) *********************** 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 : 2.076 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8537 (mp) REVERT: H 200 MET cc_start: 0.8015 (mmm) cc_final: 0.7807 (mmp) REVERT: F 99 ARG cc_start: 0.6608 (ptm160) cc_final: 0.5908 (ptm160) REVERT: F 126 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5987 (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: 0.8431 (mm110) cc_final: 0.8230 (mm-40) REVERT: A 789 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9041 (tt) REVERT: D 816 TYR cc_start: 0.7419 (t80) cc_final: 0.7155 (t80) REVERT: E 5 ASP cc_start: 0.5684 (m-30) cc_final: 0.5234 (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: 0.8623 (m100) REVERT: E 58 MET cc_start: 0.7229 (mtp) cc_final: 0.6758 (mtp) REVERT: E 78 LYS cc_start: 0.7287 (ptmt) cc_final: 0.6612 (pttt) REVERT: E 200 MET cc_start: 0.7269 (ptp) cc_final: 0.7027 (ptp) outliers start: 45 outliers final: 21 residues processed: 395 average time/residue: 0.3142 time to fit residues: 187.8706 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 : 1.918 ------------------------------------------------------------------------------- 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: 0.0010 chunk 224 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100550 restraints weight = 113171.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104144 restraints weight = 37418.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105437 restraints weight = 22539.469| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18921 Z= 0.104 Angle : 0.500 8.884 25589 Z= 0.256 Chirality : 0.038 0.167 2877 Planarity : 0.004 0.070 3155 Dihedral : 3.470 57.700 2565 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 25.05 % Favored : 72.33 % 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: 2.32 (0.18), residues: 2337 helix: 2.98 (0.13), residues: 1403 sheet: -0.47 (0.38), residues: 180 loop : -0.82 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP C 766 HIS 0.003 0.001 HIS F 60 PHE 0.011 0.001 PHE C 814 TYR 0.017 0.001 TYR B 673 ARG 0.007 0.000 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1211) hydrogen bonds : angle 3.62310 ( 3526) SS BOND : bond 0.00482 ( 12) SS BOND : angle 1.05040 ( 24) covalent geometry : bond 0.00233 (18909) covalent geometry : angle 0.49925 (25565) *********************** 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 417 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.7882 (mp) cc_final: 0.7556 (mp) REVERT: H 86 ASP cc_start: 0.0474 (OUTLIER) cc_final: 0.0066 (t70) REVERT: H 115 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (mp) REVERT: F 31 ASP cc_start: 0.7725 (m-30) cc_final: 0.7366 (p0) REVERT: F 99 ARG cc_start: 0.6639 (ptm160) cc_final: 0.6331 (ptm160) REVERT: F 126 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6118 (tm-30) REVERT: F 185 LEU cc_start: 0.8766 (tt) cc_final: 0.8496 (mp) REVERT: C 641 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7372 (mttt) REVERT: B 496 MET cc_start: 0.8588 (ptm) cc_final: 0.8304 (ttp) REVERT: A 634 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7361 (tt0) REVERT: A 789 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9069 (tt) REVERT: D 816 TYR cc_start: 0.7393 (t80) cc_final: 0.7144 (t80) REVERT: E 5 ASP cc_start: 0.5613 (m-30) cc_final: 0.5250 (m-30) REVERT: E 33 TRP cc_start: 0.8827 (m100) cc_final: 0.8554 (m100) REVERT: E 58 MET cc_start: 0.7255 (mtp) cc_final: 0.6845 (mtp) REVERT: E 78 LYS cc_start: 0.7187 (ptmt) cc_final: 0.6621 (pttt) REVERT: G 70 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5440 (tp30) REVERT: G 72 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6663 (p0) outliers start: 51 outliers final: 29 residues processed: 403 average time/residue: 0.3599 time to fit residues: 220.1090 Evaluate side-chains 361 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 327 time to evaluate : 2.331 ------------------------------------------------------------------------------- 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 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 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER 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 789 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 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 187 PHE 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 121 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 175 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN D 508 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089355 restraints weight = 82452.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093576 restraints weight = 30192.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096231 restraints weight = 17630.386| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 18921 Z= 0.257 Angle : 0.646 10.721 25589 Z= 0.337 Chirality : 0.043 0.194 2877 Planarity : 0.005 0.077 3155 Dihedral : 4.061 48.811 2565 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.00 % Allowed : 24.23 % Favored : 71.77 % 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: 1.73 (0.18), residues: 2337 helix: 2.38 (0.14), residues: 1399 sheet: -0.66 (0.37), residues: 186 loop : -0.79 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 671 HIS 0.005 0.001 HIS D 412 PHE 0.019 0.002 PHE C 814 TYR 0.021 0.002 TYR B 673 ARG 0.008 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 1211) hydrogen bonds : angle 4.12541 ( 3526) SS BOND : bond 0.00552 ( 12) SS BOND : angle 1.70790 ( 24) covalent geometry : bond 0.00603 (18909) covalent geometry : angle 0.64426 (25565) *********************** 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 429 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: -0.0041 (OUTLIER) cc_final: -0.0749 (t70) REVERT: H 199 HIS cc_start: 0.7870 (t70) cc_final: 0.7551 (t70) REVERT: F 24 MET cc_start: 0.7214 (tpp) cc_final: 0.6940 (tpp) REVERT: C 710 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 814 PHE cc_start: 0.7980 (t80) cc_final: 0.7757 (t80) REVERT: B 439 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7585 (mttp) REVERT: B 702 TYR cc_start: 0.8297 (t80) cc_final: 0.7865 (t80) REVERT: A 416 GLU cc_start: 0.5785 (mp0) cc_final: 0.5488 (mp0) REVERT: A 634 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7346 (pt0) REVERT: A 708 MET cc_start: 0.7957 (tpp) cc_final: 0.7710 (tpp) REVERT: D 463 MET cc_start: 0.8375 (mmt) cc_final: 0.7057 (mmt) REVERT: D 816 TYR cc_start: 0.7599 (t80) cc_final: 0.7387 (t80) REVERT: E 10 MET cc_start: 0.8288 (mmm) cc_final: 0.8083 (mmm) outliers start: 78 outliers final: 50 residues processed: 404 average time/residue: 0.4660 time to fit residues: 293.5653 Evaluate side-chains 373 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 5.929 ------------------------------------------------------------------------------- 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 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 400 ILE 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 609 THR 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 406 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 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 546 PHE 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 527 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 664 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 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 14 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS C 756 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.133935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096579 restraints weight = 86639.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102185 restraints weight = 31451.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103346 restraints weight = 16139.269| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18921 Z= 0.113 Angle : 0.530 10.543 25589 Z= 0.270 Chirality : 0.039 0.175 2877 Planarity : 0.004 0.070 3155 Dihedral : 3.550 22.420 2563 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.57 % Allowed : 25.41 % Favored : 72.02 % 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: 2.14 (0.18), residues: 2337 helix: 2.75 (0.14), residues: 1401 sheet: -0.49 (0.38), residues: 166 loop : -0.73 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 671 HIS 0.004 0.001 HIS H 205 PHE 0.017 0.001 PHE A 814 TYR 0.014 0.001 TYR C 424 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1211) hydrogen bonds : angle 3.71725 ( 3526) SS BOND : bond 0.00474 ( 12) SS BOND : angle 1.21826 ( 24) covalent geometry : bond 0.00255 (18909) covalent geometry : angle 0.52924 (25565) *********************** 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 401 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.0290 (OUTLIER) cc_final: -0.0503 (t0) REVERT: H 199 HIS cc_start: 0.7778 (t70) cc_final: 0.7489 (t70) REVERT: F 31 ASP cc_start: 0.7880 (m-30) cc_final: 0.7454 (p0) REVERT: C 641 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7415 (mttt) REVERT: C 814 PHE cc_start: 0.7977 (t80) cc_final: 0.7684 (t80) REVERT: B 401 LEU cc_start: 0.8547 (mt) cc_final: 0.8104 (pt) REVERT: B 549 TYR cc_start: 0.6327 (m-80) cc_final: 0.6105 (m-80) REVERT: B 702 TYR cc_start: 0.8286 (t80) cc_final: 0.7967 (t80) REVERT: B 732 TYR cc_start: 0.8464 (m-10) cc_final: 0.8159 (m-10) REVERT: A 416 GLU cc_start: 0.5872 (mp0) cc_final: 0.5623 (mp0) REVERT: A 634 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7335 (pt0) REVERT: D 463 MET cc_start: 0.8355 (mmt) cc_final: 0.7087 (mmt) REVERT: E 33 TRP cc_start: 0.8883 (m100) cc_final: 0.8505 (m100) REVERT: G 37 ARG cc_start: 0.5209 (ptt-90) cc_final: 0.4600 (ptt-90) outliers start: 50 outliers final: 40 residues processed: 386 average time/residue: 0.4592 time to fit residues: 269.5122 Evaluate side-chains 364 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 323 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 127 PHE 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 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 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 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 589 CYS 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 D residue 635 SER Chi-restraints excluded: chain D residue 664 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 122 ILE 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 73 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3791 r_free = 0.3791 target = 0.132201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094304 restraints weight = 89622.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099446 restraints weight = 32830.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100822 restraints weight = 18974.386| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18921 Z= 0.148 Angle : 0.543 11.398 25589 Z= 0.279 Chirality : 0.040 0.173 2877 Planarity : 0.004 0.059 3155 Dihedral : 3.624 31.341 2563 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.54 % Allowed : 24.44 % Favored : 72.02 % 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: 2.08 (0.18), residues: 2337 helix: 2.70 (0.14), residues: 1401 sheet: -0.49 (0.38), residues: 166 loop : -0.75 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 671 HIS 0.005 0.001 HIS D 412 PHE 0.023 0.001 PHE D 546 TYR 0.012 0.001 TYR E 156 ARG 0.007 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1211) hydrogen bonds : angle 3.81428 ( 3526) SS BOND : bond 0.00290 ( 12) SS BOND : angle 1.32140 ( 24) covalent geometry : bond 0.00348 (18909) covalent geometry : angle 0.54181 (25565) *********************** 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: 69 poor density : 343 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8064 (mp) cc_final: 0.7722 (mp) REVERT: H 24 MET cc_start: 0.7048 (tpt) cc_final: 0.6843 (tpp) REVERT: H 86 ASP cc_start: 0.0092 (OUTLIER) cc_final: -0.0580 (t0) REVERT: H 127 PHE cc_start: 0.5459 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: H 131 ARG cc_start: 0.5120 (mmp-170) cc_final: 0.4870 (mmm160) REVERT: H 199 HIS cc_start: 0.7834 (t70) cc_final: 0.7525 (t70) REVERT: H 204 ARG cc_start: 0.6970 (ttm-80) cc_final: 0.6543 (mtm110) REVERT: F 31 ASP cc_start: 0.7828 (m-30) cc_final: 0.7482 (p0) REVERT: F 65 ARG cc_start: 0.6746 (ptp-110) cc_final: 0.6064 (ptp-110) REVERT: F 204 ARG cc_start: 0.6827 (ptm160) cc_final: 0.6566 (ptm160) REVERT: C 441 LYS cc_start: 0.8410 (tmtt) cc_final: 0.7962 (mmmt) REVERT: C 641 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7423 (mttt) REVERT: C 710 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 767 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.8147 (m-90) REVERT: C 814 PHE cc_start: 0.7970 (t80) cc_final: 0.7719 (t80) REVERT: B 401 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8079 (pt) REVERT: B 702 TYR cc_start: 0.8299 (t80) cc_final: 0.7998 (t80) REVERT: A 399 THR cc_start: 0.8911 (p) cc_final: 0.8542 (m) REVERT: A 634 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7406 (pt0) REVERT: D 463 MET cc_start: 0.8410 (mmt) cc_final: 0.7140 (mmt) REVERT: E 33 TRP cc_start: 0.8873 (m100) cc_final: 0.8501 (m100) REVERT: E 200 MET cc_start: 0.7388 (ptp) cc_final: 0.7151 (ptp) REVERT: E 204 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7245 (mmm160) REVERT: G 70 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5274 (tp30) REVERT: G 149 ASN cc_start: 0.8703 (t0) cc_final: 0.8312 (t0) outliers start: 69 outliers final: 48 residues processed: 390 average time/residue: 0.2963 time to fit residues: 175.3927 Evaluate side-chains 382 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 329 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 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 C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 LEU 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 591 ILE 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 767 TRP 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 464 VAL Chi-restraints excluded: chain A residue 629 MET 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 527 MET 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 120 LEU 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 Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.0050 chunk 51 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** 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 = 0.3819 r_free = 0.3819 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096262 restraints weight = 97962.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100902 restraints weight = 32591.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103909 restraints weight = 18115.959| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18921 Z= 0.109 Angle : 0.526 11.403 25589 Z= 0.268 Chirality : 0.039 0.164 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.515 33.372 2563 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.93 % Allowed : 25.51 % Favored : 71.56 % 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: 2.25 (0.18), residues: 2337 helix: 2.84 (0.14), residues: 1403 sheet: -0.45 (0.39), residues: 166 loop : -0.67 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 671 HIS 0.004 0.001 HIS F 205 PHE 0.022 0.001 PHE D 546 TYR 0.018 0.001 TYR A 647 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1211) hydrogen bonds : angle 3.68822 ( 3526) SS BOND : bond 0.00447 ( 12) SS BOND : angle 1.95609 ( 24) covalent geometry : bond 0.00247 (18909) covalent geometry : angle 0.52296 (25565) *********************** 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 402 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8118 (mp) cc_final: 0.7778 (mp) REVERT: H 86 ASP cc_start: 0.0001 (OUTLIER) cc_final: -0.0643 (t0) REVERT: H 127 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.5184 (m-10) REVERT: H 131 ARG cc_start: 0.5037 (mmp-170) cc_final: 0.4781 (mmm160) REVERT: H 199 HIS cc_start: 0.7794 (t70) cc_final: 0.7482 (t70) REVERT: H 204 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6576 (ttp80) REVERT: F 65 ARG cc_start: 0.6693 (ptp-110) cc_final: 0.6034 (ptp-110) REVERT: F 99 ARG cc_start: 0.6217 (ptm160) cc_final: 0.5515 (ptm160) REVERT: C 641 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7476 (mttt) REVERT: C 642 GLN cc_start: 0.6452 (pp30) cc_final: 0.5762 (tm-30) REVERT: C 767 TRP cc_start: 0.8652 (OUTLIER) cc_final: 0.8162 (m-90) REVERT: C 814 PHE cc_start: 0.7991 (t80) cc_final: 0.7700 (t80) REVERT: B 401 LEU cc_start: 0.8475 (mt) cc_final: 0.8010 (pt) REVERT: B 702 TYR cc_start: 0.8270 (t80) cc_final: 0.8007 (t80) REVERT: B 732 TYR cc_start: 0.8421 (m-10) cc_final: 0.8144 (m-10) REVERT: A 399 THR cc_start: 0.8832 (p) cc_final: 0.8492 (m) REVERT: A 634 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7412 (pt0) REVERT: D 463 MET cc_start: 0.8284 (mmt) cc_final: 0.7080 (mmt) REVERT: D 633 ILE cc_start: 0.8755 (mm) cc_final: 0.8489 (tp) REVERT: D 816 TYR cc_start: 0.7504 (t80) cc_final: 0.7267 (t80) REVERT: E 200 MET cc_start: 0.7256 (ptp) cc_final: 0.6976 (ptp) REVERT: E 204 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7199 (mmm160) REVERT: G 70 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.5060 (tp30) REVERT: G 149 ASN cc_start: 0.8629 (t0) cc_final: 0.8226 (t0) outliers start: 57 outliers final: 47 residues processed: 380 average time/residue: 0.3190 time to fit residues: 185.0048 Evaluate side-chains 384 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 333 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 68 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 589 CYS Chi-restraints excluded: chain C residue 591 ILE 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 767 TRP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 464 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 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 629 MET 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 D residue 546 PHE Chi-restraints excluded: chain D residue 591 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 82 HIS Chi-restraints excluded: chain E residue 120 LEU 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 70 GLU Chi-restraints excluded: chain G residue 73 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 0.0270 chunk 150 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 133 optimal weight: 0.0770 chunk 76 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 642 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.136618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102194 restraints weight = 68038.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105376 restraints weight = 27039.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105247 restraints weight = 17407.811| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18921 Z= 0.100 Angle : 0.525 10.841 25589 Z= 0.265 Chirality : 0.038 0.162 2877 Planarity : 0.004 0.053 3155 Dihedral : 3.386 31.267 2563 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 26.28 % Favored : 71.61 % 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: 2.40 (0.18), residues: 2337 helix: 3.00 (0.14), residues: 1397 sheet: -0.49 (0.38), residues: 166 loop : -0.65 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 671 HIS 0.009 0.001 HIS H 205 PHE 0.020 0.001 PHE D 546 TYR 0.019 0.001 TYR C 816 ARG 0.008 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 1211) hydrogen bonds : angle 3.56811 ( 3526) SS BOND : bond 0.00246 ( 12) SS BOND : angle 1.45959 ( 24) covalent geometry : bond 0.00218 (18909) covalent geometry : angle 0.52368 (25565) *********************** REFINEMENT MACRO_CYCLE 8 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: 41 poor density : 362 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.7924 (mp) cc_final: 0.7589 (mp) REVERT: H 58 MET cc_start: 0.6130 (tpt) cc_final: 0.5645 (mmm) REVERT: H 86 ASP cc_start: -0.0018 (OUTLIER) cc_final: -0.0489 (t0) REVERT: H 199 HIS cc_start: 0.7728 (t70) cc_final: 0.7430 (t70) REVERT: H 204 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6531 (ttp80) REVERT: F 21 PHE cc_start: 0.7940 (t80) cc_final: 0.7735 (t80) REVERT: F 86 ASP cc_start: 0.1750 (OUTLIER) cc_final: 0.1402 (t70) REVERT: F 99 ARG cc_start: 0.6309 (ptm160) cc_final: 0.5574 (ptm160) REVERT: F 102 ARG cc_start: 0.6623 (tpt90) cc_final: 0.6188 (tpt170) REVERT: C 441 LYS cc_start: 0.8260 (tmtt) cc_final: 0.7824 (tptp) REVERT: C 460 TRP cc_start: 0.7438 (m100) cc_final: 0.7195 (m100) REVERT: C 641 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7499 (mttt) REVERT: C 642 GLN cc_start: 0.6306 (pp30) cc_final: 0.5727 (tm-30) REVERT: C 682 PHE cc_start: 0.6290 (m-80) cc_final: 0.5568 (m-80) REVERT: C 767 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.8369 (m-90) REVERT: C 814 PHE cc_start: 0.8021 (t80) cc_final: 0.7778 (t80) REVERT: B 401 LEU cc_start: 0.8477 (mt) cc_final: 0.7967 (pt) REVERT: B 638 ASP cc_start: 0.8213 (m-30) cc_final: 0.7971 (m-30) REVERT: B 702 TYR cc_start: 0.8222 (t80) cc_final: 0.8010 (t80) REVERT: B 732 TYR cc_start: 0.8364 (m-10) cc_final: 0.8097 (m-10) REVERT: B 758 VAL cc_start: 0.9261 (m) cc_final: 0.9045 (p) REVERT: A 399 THR cc_start: 0.8812 (p) cc_final: 0.8533 (m) REVERT: A 416 GLU cc_start: 0.6503 (pm20) cc_final: 0.5872 (mp0) REVERT: A 502 ILE cc_start: 0.8879 (mp) cc_final: 0.8538 (mm) REVERT: A 634 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7393 (pt0) REVERT: A 705 GLU cc_start: 0.8057 (mp0) cc_final: 0.7639 (mp0) REVERT: D 463 MET cc_start: 0.8304 (mmt) cc_final: 0.7069 (mmt) REVERT: D 633 ILE cc_start: 0.8730 (mm) cc_final: 0.8496 (tp) REVERT: D 816 TYR cc_start: 0.7396 (t80) cc_final: 0.7157 (t80) REVERT: E 33 TRP cc_start: 0.8808 (m100) cc_final: 0.8476 (m100) REVERT: G 24 MET cc_start: 0.8005 (mmm) cc_final: 0.7740 (mmm) REVERT: G 99 ARG cc_start: 0.5084 (ttm110) cc_final: 0.4151 (ptm160) REVERT: G 149 ASN cc_start: 0.8566 (t0) cc_final: 0.8147 (t0) outliers start: 41 outliers final: 29 residues processed: 389 average time/residue: 0.3042 time to fit residues: 179.4939 Evaluate side-chains 365 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 333 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 473 ASP 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 685 THR Chi-restraints excluded: chain A residue 746 VAL 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 642 GLN 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 G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 212 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094432 restraints weight = 93456.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098945 restraints weight = 32018.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101791 restraints weight = 18186.887| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18921 Z= 0.151 Angle : 0.569 11.050 25589 Z= 0.291 Chirality : 0.040 0.229 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.539 32.890 2563 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.46 % Allowed : 26.64 % Favored : 70.89 % 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: 2.18 (0.18), residues: 2337 helix: 2.80 (0.14), residues: 1401 sheet: -0.60 (0.37), residues: 186 loop : -0.71 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 671 HIS 0.008 0.001 HIS H 205 PHE 0.024 0.001 PHE F 107 TYR 0.015 0.001 TYR A 647 ARG 0.012 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1211) hydrogen bonds : angle 3.74630 ( 3526) SS BOND : bond 0.00309 ( 12) SS BOND : angle 1.52757 ( 24) covalent geometry : bond 0.00358 (18909) covalent geometry : angle 0.56780 (25565) *********************** REFINEMENT MACRO_CYCLE 9 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 382 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.8083 (mp) cc_final: 0.7757 (mp) REVERT: H 58 MET cc_start: 0.6122 (tpt) cc_final: 0.5659 (mmm) REVERT: H 86 ASP cc_start: 0.0078 (OUTLIER) cc_final: -0.0447 (t0) REVERT: H 204 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6536 (mtm110) REVERT: F 65 ARG cc_start: 0.6336 (ptp-110) cc_final: 0.6068 (ptp-110) REVERT: F 86 ASP cc_start: 0.1543 (OUTLIER) cc_final: 0.1205 (t70) REVERT: F 99 ARG cc_start: 0.6316 (ptm160) cc_final: 0.5663 (ptm160) REVERT: F 102 ARG cc_start: 0.6716 (tpt90) cc_final: 0.6230 (tpt170) REVERT: F 144 SER cc_start: 0.8543 (m) cc_final: 0.8268 (p) REVERT: F 203 ASP cc_start: 0.8100 (t0) cc_final: 0.7749 (t0) REVERT: C 441 LYS cc_start: 0.8299 (tmtt) cc_final: 0.7860 (tptp) REVERT: C 641 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7563 (mttt) REVERT: C 710 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7688 (mt-10) REVERT: C 767 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.8325 (m-90) REVERT: C 814 PHE cc_start: 0.7998 (t80) cc_final: 0.7776 (t80) REVERT: B 401 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8040 (pt) REVERT: B 674 MET cc_start: 0.8158 (mtt) cc_final: 0.7822 (mtt) REVERT: B 702 TYR cc_start: 0.8295 (t80) cc_final: 0.8013 (t80) REVERT: B 755 GLU cc_start: 0.8495 (mp0) cc_final: 0.8048 (mp0) REVERT: A 399 THR cc_start: 0.8809 (p) cc_final: 0.8479 (m) REVERT: A 416 GLU cc_start: 0.6585 (pm20) cc_final: 0.6127 (mp0) REVERT: A 634 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7433 (pt0) REVERT: D 463 MET cc_start: 0.8295 (mmt) cc_final: 0.7042 (mmt) REVERT: D 633 ILE cc_start: 0.8769 (mm) cc_final: 0.8533 (tp) REVERT: D 816 TYR cc_start: 0.7484 (t80) cc_final: 0.7265 (t80) REVERT: E 6 ARG cc_start: 0.5982 (mmm160) cc_final: 0.5540 (tpt-90) REVERT: G 70 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.5057 (tp30) REVERT: G 99 ARG cc_start: 0.5140 (ttm110) cc_final: 0.4237 (ptm160) REVERT: G 149 ASN cc_start: 0.8684 (t0) cc_final: 0.8297 (t0) outliers start: 48 outliers final: 36 residues processed: 367 average time/residue: 0.3006 time to fit residues: 166.3373 Evaluate side-chains 360 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE 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 767 TRP 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 443 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 746 VAL 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 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 195 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 86 optimal weight: 0.0670 chunk 208 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092648 restraints weight = 105871.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097246 restraints weight = 33775.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100139 restraints weight = 18490.436| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18921 Z= 0.115 Angle : 0.558 12.107 25589 Z= 0.283 Chirality : 0.039 0.203 2877 Planarity : 0.004 0.079 3155 Dihedral : 3.517 32.277 2563 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.31 % Allowed : 27.16 % Favored : 70.53 % 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: 2.21 (0.18), residues: 2337 helix: 2.84 (0.14), residues: 1397 sheet: -0.56 (0.39), residues: 166 loop : -0.72 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 671 HIS 0.007 0.001 HIS H 205 PHE 0.021 0.001 PHE D 546 TYR 0.021 0.001 TYR C 816 ARG 0.009 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1211) hydrogen bonds : angle 3.70731 ( 3526) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.52872 ( 24) covalent geometry : bond 0.00264 (18909) covalent geometry : angle 0.55668 (25565) ********************** REFINEMENT MACRO_CYCLE 10 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 385 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLN cc_start: 0.7632 (mt0) cc_final: 0.7402 (mt0) REVERT: H 12 LEU cc_start: 0.8015 (mp) cc_final: 0.7673 (mp) REVERT: H 58 MET cc_start: 0.6116 (tpt) cc_final: 0.5640 (mmm) REVERT: H 86 ASP cc_start: 0.0103 (OUTLIER) cc_final: -0.0425 (t0) REVERT: H 204 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.6459 (mtm110) REVERT: F 65 ARG cc_start: 0.6269 (ptp-110) cc_final: 0.5983 (ptp-110) REVERT: F 86 ASP cc_start: 0.1626 (OUTLIER) cc_final: 0.1249 (t70) REVERT: F 99 ARG cc_start: 0.6329 (ptm160) cc_final: 0.5667 (ptm160) REVERT: F 102 ARG cc_start: 0.6603 (tpt90) cc_final: 0.6014 (tpt170) REVERT: F 203 ASP cc_start: 0.8117 (t0) cc_final: 0.7790 (t0) REVERT: C 441 LYS cc_start: 0.8320 (tmtt) cc_final: 0.7874 (tptp) REVERT: C 641 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7572 (mttt) REVERT: C 710 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 767 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.8239 (m-90) REVERT: C 814 PHE cc_start: 0.8019 (t80) cc_final: 0.7776 (t80) REVERT: B 401 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8044 (pt) REVERT: B 638 ASP cc_start: 0.8222 (m-30) cc_final: 0.7899 (m-30) REVERT: B 674 MET cc_start: 0.8210 (mtt) cc_final: 0.7866 (mtt) REVERT: B 702 TYR cc_start: 0.8283 (t80) cc_final: 0.8008 (t80) REVERT: B 732 TYR cc_start: 0.8476 (m-10) cc_final: 0.8167 (m-10) REVERT: B 755 GLU cc_start: 0.8455 (mp0) cc_final: 0.7962 (mp0) REVERT: A 399 THR cc_start: 0.8815 (p) cc_final: 0.8541 (m) REVERT: A 416 GLU cc_start: 0.6686 (pm20) cc_final: 0.6232 (mp0) REVERT: A 634 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7402 (pt0) REVERT: A 705 GLU cc_start: 0.8156 (mp0) cc_final: 0.7654 (mp0) REVERT: D 463 MET cc_start: 0.8306 (mmt) cc_final: 0.7038 (mmt) REVERT: D 633 ILE cc_start: 0.8733 (mm) cc_final: 0.8486 (tp) REVERT: D 816 TYR cc_start: 0.7455 (t80) cc_final: 0.7230 (t80) REVERT: E 200 MET cc_start: 0.7352 (ptp) cc_final: 0.7111 (ptp) REVERT: E 204 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7137 (mmm160) REVERT: G 70 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.5123 (tp30) REVERT: G 99 ARG cc_start: 0.5147 (ttm110) cc_final: 0.4219 (ptm160) REVERT: G 149 ASN cc_start: 0.8638 (t0) cc_final: 0.8224 (t0) outliers start: 45 outliers final: 39 residues processed: 371 average time/residue: 0.3254 time to fit residues: 184.1116 Evaluate side-chains 371 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 767 TRP 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 464 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 LEU 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 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 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 195 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 202 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093461 restraints weight = 76770.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097669 restraints weight = 28699.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100266 restraints weight = 16937.224| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18921 Z= 0.124 Angle : 0.572 12.171 25589 Z= 0.291 Chirality : 0.039 0.195 2877 Planarity : 0.004 0.053 3155 Dihedral : 3.554 32.995 2563 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.62 % Allowed : 27.16 % Favored : 70.23 % 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: 2.16 (0.18), residues: 2337 helix: 2.80 (0.14), residues: 1397 sheet: -0.61 (0.38), residues: 166 loop : -0.73 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 671 HIS 0.007 0.001 HIS H 205 PHE 0.021 0.001 PHE D 546 TYR 0.014 0.001 TYR E 128 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 1211) hydrogen bonds : angle 3.74319 ( 3526) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.48091 ( 24) covalent geometry : bond 0.00288 (18909) covalent geometry : angle 0.57054 (25565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8223.08 seconds wall clock time: 146 minutes 32.37 seconds (8792.37 seconds total)