Starting phenix.real_space_refine on Wed Jan 22 10:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6a_44251/01_2025/9b6a_44251.cif" } resolution = 3.35 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= 0.004 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 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.81 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.19 residue: pdb=" N APHE B 623 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.49 residue: pdb=" N APHE D 623 " occ=0.73 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.27 Time building chain proxies: 15.28, per 1000 atoms: 0.83 Number of scatterers: 18493 At special positions: 0 Unit cell: (114.8, 108.24, 145.96, 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=2.03 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 3.8 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: 90 helices and 24 sheets defined 60.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.693A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.599A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.594A 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 removed outlier: 3.643A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.917A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.546A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.610A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.704A 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 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.809A 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 629 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.655A 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 792 through 825 removed outlier: 3.602A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.786A 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: 3.856A 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 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 removed outlier: 3.543A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 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 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.841A 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 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.732A 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 629 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 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 792 through 825 removed outlier: 3.631A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.077A 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 488 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.897A 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 661 removed outlier: 4.287A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) 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 removed outlier: 3.525A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) 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: 3.751A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.701A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 3.986A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.773A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.645A 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 removed outlier: 3.603A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 407 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: 3.733A 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: 6.499A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.704A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.521A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 5.222A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 removed outlier: 5.222A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.446A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.546A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB8, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.805A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.701A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 489 through 498 removed outlier: 6.795A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.462A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 78 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 77 through 79 1191 hydrogen bonds defined for protein. 3466 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: 6.42 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5728 1.36 - 1.49: 5064 1.49 - 1.62: 7908 1.62 - 1.75: 2 1.75 - 1.88: 207 Bond restraints: 18909 Sorted by residual: bond pdb=" CG PRO D 548 " pdb=" CD PRO D 548 " ideal model delta sigma weight residual 1.503 1.230 0.273 3.40e-02 8.65e+02 6.45e+01 bond pdb=" N PRO D 548 " pdb=" CD PRO D 548 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" CB PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.19e+01 bond pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.49e-02 4.50e+03 1.15e+01 bond pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.61e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 25483 3.04 - 6.08: 72 6.08 - 9.11: 5 9.11 - 12.15: 1 12.15 - 15.19: 4 Bond angle restraints: 25565 Sorted by residual: angle pdb=" N PRO D 548 " pdb=" CD PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 103.20 88.45 14.75 1.50e+00 4.44e-01 9.67e+01 angle pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " pdb=" CG PRO D 548 " ideal model delta sigma weight residual 104.50 89.31 15.19 1.90e+00 2.77e-01 6.39e+01 angle pdb=" N PRO D 548 " pdb=" CA PRO D 548 " pdb=" CB PRO D 548 " ideal model delta sigma weight residual 103.51 95.87 7.64 9.60e-01 1.09e+00 6.33e+01 angle pdb=" CA CYS G 77 " pdb=" CB CYS G 77 " pdb=" SG CYS G 77 " ideal model delta sigma weight residual 114.40 128.68 -14.28 2.30e+00 1.89e-01 3.86e+01 angle pdb=" CA PRO B 745 " pdb=" N PRO B 745 " pdb=" CD PRO B 745 " ideal model delta sigma weight residual 112.00 103.78 8.22 1.40e+00 5.10e-01 3.45e+01 ... (remaining 25560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9503 17.81 - 35.61: 1160 35.61 - 53.42: 339 53.42 - 71.23: 43 71.23 - 89.04: 22 Dihedral angle restraints: 11067 sinusoidal: 4227 harmonic: 6840 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 176.71 -83.71 1 1.00e+01 1.00e-02 8.55e+01 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 93.00 173.65 -80.65 1 1.00e+01 1.00e-02 8.04e+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 93.00 168.64 -75.64 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 11064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2386 0.051 - 0.101: 422 0.101 - 0.152: 68 0.152 - 0.202: 0 0.202 - 0.253: 1 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA CYS G 77 " pdb=" N CYS G 77 " pdb=" C CYS G 77 " pdb=" CB CYS G 77 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE D 474 " pdb=" N ILE D 474 " pdb=" C ILE D 474 " pdb=" CB ILE D 474 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2874 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " 0.087 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO B 745 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO B 679 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 678 " -0.036 5.00e-02 4.00e+02 5.29e-02 4.49e+00 pdb=" N PRO D 679 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.026 5.00e-02 4.00e+02 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1176 2.74 - 3.28: 18459 3.28 - 3.82: 32517 3.82 - 4.36: 35922 4.36 - 4.90: 63568 Nonbonded interactions: 151642 Sorted by model distance: nonbonded pdb=" O SER D 631 " pdb=" OG SER D 631 " model vdw 2.196 3.040 nonbonded pdb=" O ALA E 20 " pdb=" OG SER E 186 " model vdw 2.222 3.040 nonbonded pdb=" O GLN H 9 " pdb=" OG1 THR H 13 " model vdw 2.225 3.040 nonbonded pdb=" O PHE E 107 " pdb=" OG SER E 148 " model vdw 2.266 3.040 nonbonded pdb=" O PRO C 520 " pdb=" ND2 ASN C 619 " model vdw 2.268 3.120 ... (remaining 151637 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=0.19 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.970 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 48.190 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 0.273 18909 Z= 0.185 Angle : 0.496 15.190 25565 Z= 0.272 Chirality : 0.038 0.253 2877 Planarity : 0.004 0.127 3155 Dihedral : 16.789 89.036 6665 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.26 % Allowed : 24.74 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.18), residues: 2337 helix: 2.81 (0.14), residues: 1393 sheet: -0.66 (0.41), residues: 146 loop : -0.86 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 671 HIS 0.004 0.001 HIS G 132 PHE 0.015 0.001 PHE C 438 TYR 0.010 0.001 TYR A 440 ARG 0.004 0.000 ARG E 99 *********************** 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 296 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: D 619 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7611 (t0) REVERT: G 95 GLU cc_start: 0.5014 (tm-30) cc_final: 0.3985 (tt0) outliers start: 5 outliers final: 3 residues processed: 293 average time/residue: 0.3371 time to fit residues: 146.3836 Evaluate side-chains 281 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 713 GLU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 181 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN B 756 GLN A 756 GLN D 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.179711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144946 restraints weight = 53680.158| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.38 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18909 Z= 0.128 Angle : 0.439 10.127 25565 Z= 0.233 Chirality : 0.037 0.141 2877 Planarity : 0.004 0.086 3155 Dihedral : 3.572 53.285 2571 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.54 % Allowed : 23.87 % Favored : 74.59 % 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: 2.51 (0.18), residues: 2337 helix: 3.20 (0.14), residues: 1393 sheet: -0.62 (0.41), residues: 146 loop : -0.79 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 671 HIS 0.004 0.001 HIS G 132 PHE 0.011 0.001 PHE E 21 TYR 0.011 0.001 TYR A 647 ARG 0.003 0.000 ARG E 99 *********************** 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 345 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 738 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7870 (mtpp) REVERT: B 486 GLU cc_start: 0.7032 (tp30) cc_final: 0.6819 (tp30) REVERT: D 490 ASP cc_start: 0.6477 (p0) cc_final: 0.5964 (t0) outliers start: 30 outliers final: 23 residues processed: 331 average time/residue: 0.3325 time to fit residues: 164.4544 Evaluate side-chains 310 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 0.0010 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.174962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140560 restraints weight = 64163.792| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.21 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18909 Z= 0.230 Angle : 0.490 9.290 25565 Z= 0.259 Chirality : 0.040 0.156 2877 Planarity : 0.004 0.075 3155 Dihedral : 3.874 58.613 2567 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.82 % Allowed : 22.79 % Favored : 74.38 % 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: 2.19 (0.18), residues: 2337 helix: 2.89 (0.14), residues: 1403 sheet: -0.74 (0.40), residues: 146 loop : -0.87 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.005 0.001 HIS F 205 PHE 0.016 0.001 PHE C 682 TYR 0.015 0.001 TYR C 424 ARG 0.014 0.000 ARG H 6 *********************** 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 341 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7522 (m) cc_final: 0.7211 (m) REVERT: H 209 ARG cc_start: 0.5701 (mmm-85) cc_final: 0.5107 (ttp-110) REVERT: C 738 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7855 (mtpp) outliers start: 55 outliers final: 38 residues processed: 322 average time/residue: 0.3342 time to fit residues: 160.9028 Evaluate side-chains 308 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 175 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 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 = 0.3914 r_free = 0.3914 target = 0.175134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.141555 restraints weight = 51187.951| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.26 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18909 Z= 0.170 Angle : 0.467 16.289 25565 Z= 0.244 Chirality : 0.039 0.186 2877 Planarity : 0.003 0.067 3155 Dihedral : 3.753 54.924 2567 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 23.56 % Favored : 73.56 % 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: 2.93 (0.14), residues: 1403 sheet: -0.79 (0.40), residues: 146 loop : -0.89 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 551 HIS 0.005 0.001 HIS G 132 PHE 0.015 0.001 PHE C 682 TYR 0.013 0.001 TYR C 424 ARG 0.006 0.000 ARG F 37 *********************** 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 349 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7463 (m) cc_final: 0.7139 (m) REVERT: H 151 ILE cc_start: 0.8690 (mm) cc_final: 0.8479 (mm) REVERT: H 209 ARG cc_start: 0.5694 (mmm-85) cc_final: 0.5088 (ttp-110) REVERT: A 408 MET cc_start: 0.5324 (mmm) cc_final: 0.5009 (mmt) outliers start: 56 outliers final: 43 residues processed: 333 average time/residue: 0.3252 time to fit residues: 163.2989 Evaluate side-chains 322 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 HIS B ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.173429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136783 restraints weight = 48788.982| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.24 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18909 Z= 0.172 Angle : 0.472 13.868 25565 Z= 0.245 Chirality : 0.038 0.207 2877 Planarity : 0.003 0.063 3155 Dihedral : 3.721 54.640 2567 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.18 % Allowed : 23.72 % Favored : 73.10 % 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: 2.27 (0.18), residues: 2337 helix: 3.01 (0.14), residues: 1391 sheet: -0.85 (0.40), residues: 146 loop : -0.86 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.006 0.001 HIS G 132 PHE 0.015 0.001 PHE C 682 TYR 0.013 0.001 TYR A 647 ARG 0.006 0.000 ARG F 37 *********************** 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 354 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7464 (m) cc_final: 0.7147 (m) REVERT: H 209 ARG cc_start: 0.5666 (mmm-85) cc_final: 0.5029 (ttp-110) REVERT: C 756 GLN cc_start: 0.6777 (pt0) cc_final: 0.6359 (pt0) REVERT: B 745 PRO cc_start: 0.7403 (Cg_exo) cc_final: 0.7166 (Cg_endo) REVERT: A 627 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: A 641 LYS cc_start: 0.7331 (mtmt) cc_final: 0.6360 (mmtm) outliers start: 62 outliers final: 45 residues processed: 337 average time/residue: 0.3299 time to fit residues: 167.3759 Evaluate side-chains 322 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 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 = 0.3917 r_free = 0.3917 target = 0.175574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140241 restraints weight = 55080.692| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.36 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 18909 Z= 0.153 Angle : 0.460 12.246 25565 Z= 0.239 Chirality : 0.038 0.218 2877 Planarity : 0.003 0.059 3155 Dihedral : 3.631 54.304 2567 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.08 % Allowed : 23.56 % Favored : 73.36 % 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: 2.34 (0.18), residues: 2337 helix: 3.09 (0.14), residues: 1391 sheet: -0.85 (0.39), residues: 150 loop : -0.87 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.003 0.001 HIS H 205 PHE 0.014 0.001 PHE C 682 TYR 0.015 0.001 TYR A 440 ARG 0.005 0.000 ARG F 37 *********************** 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 350 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7411 (m) cc_final: 0.7065 (m) REVERT: H 209 ARG cc_start: 0.5617 (mmm-85) cc_final: 0.4962 (ttp-110) REVERT: C 756 GLN cc_start: 0.6742 (pt0) cc_final: 0.6296 (pt0) REVERT: A 408 MET cc_start: 0.5279 (mmm) cc_final: 0.4875 (mmt) REVERT: A 627 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 641 LYS cc_start: 0.7404 (mtmt) cc_final: 0.6360 (mmtm) REVERT: A 660 ARG cc_start: 0.6846 (ttm-80) cc_final: 0.6359 (ttp-110) outliers start: 60 outliers final: 45 residues processed: 334 average time/residue: 0.3260 time to fit residues: 164.0844 Evaluate side-chains 318 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 155 VAL 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: 0.8980 chunk 113 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.0470 chunk 51 optimal weight: 0.0980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN B ** G 60 HIS ** 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 = 0.3924 r_free = 0.3924 target = 0.176166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139520 restraints weight = 61112.421| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.41 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 18909 Z= 0.131 Angle : 0.441 10.471 25565 Z= 0.228 Chirality : 0.037 0.207 2877 Planarity : 0.003 0.038 3155 Dihedral : 3.425 52.638 2567 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 24.49 % Favored : 73.36 % 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: 2.52 (0.18), residues: 2337 helix: 3.25 (0.14), residues: 1393 sheet: -0.71 (0.38), residues: 170 loop : -0.85 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.003 0.001 HIS H 205 PHE 0.011 0.001 PHE C 546 TYR 0.011 0.001 TYR A 647 ARG 0.004 0.000 ARG H 37 *********************** 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 342 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7356 (m) cc_final: 0.7015 (m) REVERT: H 209 ARG cc_start: 0.5596 (mmm-85) cc_final: 0.4927 (ttp-110) REVERT: C 756 GLN cc_start: 0.6840 (pt0) cc_final: 0.6343 (pt0) REVERT: A 503 MET cc_start: 0.7721 (ptt) cc_final: 0.7476 (ppp) REVERT: A 641 LYS cc_start: 0.7420 (mtmt) cc_final: 0.6349 (mmtm) REVERT: A 660 ARG cc_start: 0.6774 (ttm-80) cc_final: 0.6315 (ttp-110) REVERT: G 95 GLU cc_start: 0.4689 (tm-30) cc_final: 0.4015 (tt0) outliers start: 42 outliers final: 29 residues processed: 335 average time/residue: 0.3200 time to fit residues: 162.3948 Evaluate side-chains 306 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS A 756 GLN E 9 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150919 restraints weight = 41258.526| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 4.55 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 18909 Z= 0.144 Angle : 0.452 11.037 25565 Z= 0.235 Chirality : 0.038 0.225 2877 Planarity : 0.003 0.040 3155 Dihedral : 3.189 15.181 2563 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.21 % Allowed : 24.54 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.18), residues: 2337 helix: 3.24 (0.14), residues: 1393 sheet: -0.64 (0.39), residues: 160 loop : -0.85 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 671 HIS 0.003 0.001 HIS H 205 PHE 0.010 0.001 PHE D 495 TYR 0.018 0.001 TYR A 440 ARG 0.006 0.000 ARG H 37 *********************** 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 327 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7270 (m) cc_final: 0.6922 (m) REVERT: H 209 ARG cc_start: 0.5630 (mmm-85) cc_final: 0.4871 (ttp-110) REVERT: C 756 GLN cc_start: 0.6880 (pt0) cc_final: 0.6369 (pt0) REVERT: A 627 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: A 641 LYS cc_start: 0.7412 (mtmt) cc_final: 0.6275 (mmtm) REVERT: A 660 ARG cc_start: 0.6783 (ttm-80) cc_final: 0.6303 (ttp-110) REVERT: E 23 LEU cc_start: 0.8477 (mt) cc_final: 0.8222 (mt) REVERT: E 211 THR cc_start: 0.7018 (t) cc_final: 0.6813 (p) outliers start: 43 outliers final: 38 residues processed: 317 average time/residue: 0.3537 time to fit residues: 170.8334 Evaluate side-chains 320 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 212 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136686 restraints weight = 54033.289| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.32 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18909 Z= 0.172 Angle : 0.477 11.646 25565 Z= 0.247 Chirality : 0.039 0.215 2877 Planarity : 0.003 0.039 3155 Dihedral : 3.280 16.336 2563 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 24.33 % Favored : 73.10 % 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: 2.42 (0.18), residues: 2337 helix: 3.14 (0.14), residues: 1393 sheet: -0.67 (0.39), residues: 160 loop : -0.87 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 671 HIS 0.003 0.001 HIS F 205 PHE 0.018 0.001 PHE C 682 TYR 0.013 0.001 TYR A 647 ARG 0.005 0.000 ARG H 37 *********************** 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 335 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7351 (m) cc_final: 0.7019 (m) REVERT: H 209 ARG cc_start: 0.5662 (mmm-85) cc_final: 0.4936 (ttp-110) REVERT: C 756 GLN cc_start: 0.6878 (pt0) cc_final: 0.6329 (pt0) REVERT: A 627 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: G 95 GLU cc_start: 0.4720 (tm-30) cc_final: 0.4081 (tt0) outliers start: 50 outliers final: 43 residues processed: 324 average time/residue: 0.3466 time to fit residues: 171.1894 Evaluate side-chains 322 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.176302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138747 restraints weight = 61849.972| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.56 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18909 Z= 0.165 Angle : 0.480 11.744 25565 Z= 0.248 Chirality : 0.039 0.203 2877 Planarity : 0.003 0.039 3155 Dihedral : 3.283 14.195 2563 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.41 % Allowed : 24.49 % Favored : 73.10 % 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: 2.33 (0.18), residues: 2337 helix: 3.04 (0.14), residues: 1405 sheet: -0.71 (0.39), residues: 160 loop : -0.90 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 671 HIS 0.003 0.001 HIS H 205 PHE 0.018 0.001 PHE C 682 TYR 0.014 0.001 TYR C 647 ARG 0.005 0.000 ARG H 37 ********************** 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 328 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 THR cc_start: 0.7409 (m) cc_final: 0.7064 (m) REVERT: H 209 ARG cc_start: 0.5646 (mmm-85) cc_final: 0.4936 (ttp-110) REVERT: C 756 GLN cc_start: 0.6906 (pt0) cc_final: 0.6351 (pt0) REVERT: A 627 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 660 ARG cc_start: 0.6796 (ttm-80) cc_final: 0.6351 (ttp-110) REVERT: G 95 GLU cc_start: 0.4713 (tm-30) cc_final: 0.4090 (tt0) outliers start: 47 outliers final: 44 residues processed: 318 average time/residue: 0.3196 time to fit residues: 154.8255 Evaluate side-chains 321 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 202 optimal weight: 0.0050 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.177401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137841 restraints weight = 44025.479| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.29 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18909 Z= 0.140 Angle : 0.465 11.482 25565 Z= 0.240 Chirality : 0.038 0.192 2877 Planarity : 0.003 0.046 3155 Dihedral : 3.224 13.821 2563 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.16 % Allowed : 25.00 % Favored : 72.84 % 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: 2.48 (0.18), residues: 2337 helix: 3.20 (0.14), residues: 1395 sheet: -0.64 (0.39), residues: 160 loop : -0.86 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 671 HIS 0.003 0.001 HIS H 205 PHE 0.016 0.001 PHE C 438 TYR 0.012 0.001 TYR C 647 ARG 0.006 0.000 ARG H 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6544.05 seconds wall clock time: 121 minutes 41.09 seconds (7301.09 seconds total)