Starting phenix.real_space_refine on Sun May 18 11:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3z_17400/05_2025/8p3z_17400.cif" } resolution = 3.46 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= -0.001 sd= 0.048 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 120 5.16 5 C 11100 2.51 5 N 2740 2.21 5 O 3014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16974 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2874 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 2843 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 390, 2843 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 2894 Chain: "C" Number of atoms: 2885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 2874 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 394, 2874 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2925 Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2853 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 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: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 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: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 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: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 574 " occ=0.50 residue: pdb=" N APHE C 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 574 " occ=0.50 Time building chain proxies: 12.29, per 1000 atoms: 0.72 Number of scatterers: 16974 At special positions: 0 Unit cell: (117.086, 140.214, 147.441, 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 120 16.00 O 3014 8.00 N 2740 7.00 C 11100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.9 seconds 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 28 sheets defined 60.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.818A 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 removed outlier: 3.578A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.751A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.611A pdb=" N GLU A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 551' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 removed outlier: 3.543A pdb=" N ARG A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) 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 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.627A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 821 removed outlier: 3.765A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.531A pdb=" N MET B 414 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.913A 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 removed outlier: 3.636A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.754A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.647A pdb=" N TRP B 578 " --> pdb=" O BPHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 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 757 removed outlier: 3.523A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 823 removed outlier: 3.730A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.801A 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 removed outlier: 3.639A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.758A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.744A 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 626 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.635A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.593A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.715A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.809A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.622A 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 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.502A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.625A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 removed outlier: 3.743A pdb=" N LEU E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 134 through 161 Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.914A pdb=" N MET F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 105 through 124 Processing helix chain 'F' and resid 133 through 161 removed outlier: 3.586A pdb=" N ALA F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 209 removed outlier: 3.933A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 124 Processing helix chain 'G' and resid 133 through 160 removed outlier: 3.693A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 28 Processing helix chain 'H' and resid 93 through 104 Processing helix chain 'H' and resid 105 through 127 removed outlier: 3.944A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 Processing helix chain 'H' and resid 177 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.467A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.467A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.824A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.364A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.364A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 394 through 399 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.450A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.450A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.466A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.594A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.520A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.520A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC5, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.780A pdb=" N LYS H 78 " --> pdb=" O THR H 66 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3258 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: 5.41 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2626 1.30 - 1.43: 4979 1.43 - 1.57: 9561 1.57 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 17358 Sorted by residual: bond pdb=" C TYR D 768 " pdb=" N ASP D 769 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.35e-02 5.49e+03 7.35e+01 bond pdb=" C PHE C 584 " pdb=" O PHE C 584 " ideal model delta sigma weight residual 1.237 1.171 0.065 1.19e-02 7.06e+03 3.01e+01 bond pdb=" CA SER C 592 " pdb=" CB SER C 592 " ideal model delta sigma weight residual 1.535 1.469 0.066 1.21e-02 6.83e+03 2.96e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.536 1.460 0.077 1.48e-02 4.57e+03 2.67e+01 bond pdb=" CA SER C 788 " pdb=" CB SER C 788 " ideal model delta sigma weight residual 1.533 1.455 0.078 1.60e-02 3.91e+03 2.40e+01 ... (remaining 17353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 20531 2.46 - 4.92: 2860 4.92 - 7.39: 170 7.39 - 9.85: 7 9.85 - 12.31: 3 Bond angle restraints: 23571 Sorted by residual: angle pdb=" N GLU C 772 " pdb=" CA GLU C 772 " pdb=" C GLU C 772 " ideal model delta sigma weight residual 113.61 102.70 10.91 1.50e+00 4.44e-01 5.29e+01 angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 113.88 105.63 8.25 1.23e+00 6.61e-01 4.50e+01 angle pdb=" N LEU C 803 " pdb=" CA LEU C 803 " pdb=" C LEU C 803 " ideal model delta sigma weight residual 111.82 104.61 7.21 1.16e+00 7.43e-01 3.87e+01 angle pdb=" N LEU A 803 " pdb=" CA LEU A 803 " pdb=" C LEU A 803 " ideal model delta sigma weight residual 111.82 104.91 6.91 1.16e+00 7.43e-01 3.55e+01 angle pdb=" N SER F 104 " pdb=" CA SER F 104 " pdb=" C SER F 104 " ideal model delta sigma weight residual 110.48 102.21 8.27 1.48e+00 4.57e-01 3.12e+01 ... (remaining 23566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8910 17.67 - 35.33: 858 35.33 - 53.00: 145 53.00 - 70.66: 21 70.66 - 88.33: 13 Dihedral angle restraints: 9947 sinusoidal: 3419 harmonic: 6528 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 22.08 70.92 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 38.19 54.81 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 41.86 51.14 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 9944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1128 0.077 - 0.154: 1084 0.154 - 0.231: 477 0.231 - 0.309: 40 0.309 - 0.386: 4 Chirality restraints: 2733 Sorted by residual: chirality pdb=" CB VAL A 601 " pdb=" CA VAL A 601 " pdb=" CG1 VAL A 601 " pdb=" CG2 VAL A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA CYS A 589 " pdb=" N CYS A 589 " pdb=" C CYS A 589 " pdb=" CB CYS A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PRO D 717 " pdb=" N PRO D 717 " pdb=" C PRO D 717 " pdb=" CB PRO D 717 " both_signs ideal model delta sigma weight residual False 2.72 3.04 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2730 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 574 " -0.031 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C BPHE B 574 " 0.111 2.00e-02 2.50e+03 pdb=" O BPHE B 574 " -0.041 2.00e-02 2.50e+03 pdb=" N ASN B 575 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 420 " -0.528 9.50e-02 1.11e+02 2.37e-01 3.42e+01 pdb=" NE ARG A 420 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 420 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 420 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 420 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 420 " -0.515 9.50e-02 1.11e+02 2.31e-01 3.27e+01 pdb=" NE ARG D 420 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 420 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 420 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 420 " -0.020 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4044 2.77 - 3.30: 17664 3.30 - 3.83: 27036 3.83 - 4.37: 33920 4.37 - 4.90: 54855 Nonbonded interactions: 137519 Sorted by model distance: nonbonded pdb=" N VAL B 395 " pdb=" O LYS B 439 " model vdw 2.233 3.120 nonbonded pdb=" O LYS G 129 " pdb=" OG1 THR G 130 " model vdw 2.236 3.040 nonbonded pdb=" O SER G 104 " pdb=" N ILE G 106 " model vdw 2.257 3.120 nonbonded pdb=" N VAL D 395 " pdb=" O LYS D 439 " model vdw 2.259 3.120 nonbonded pdb=" O ASP D 427 " pdb=" OE1 GLU D 431 " model vdw 2.290 3.040 ... (remaining 137514 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 505 or (resid 506 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 573 or resid 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 626 or resid 636 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 82 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 393 through 505 or (resid 506 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 549 or (resid 550 \ and (name N or name CA or name C or name O or name CB )) or resid 551 or (resid \ 569 and (name N or name CA or name C or name O or name CB )) or resid 570 throug \ h 573 or resid 575 or (resid 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name \ C or name O or name CB )) or resid 595 through 636 or (resid 637 through 638 and \ (name N or name CA or name C or name O or name CB )) or resid 639 through 823)) \ selection = (chain 'C' and (resid 393 through 505 or (resid 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 511 through 549 or (resid 550 and (name N \ or name CA or name C or name O or name CB )) or resid 551 through 573 or resid 5 \ 75 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 626 or resid 636 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 (resi \ d 819 through 823 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 or (resid 569 and (name N or name CA o \ r name C or name O or name CB )) or resid 570 through 573 or resid 575 or (resid \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 throu \ gh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) or \ resid 595 through 626 or resid 636 through 773 or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 16 \ 2 or resid 173 through 210)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.530 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 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 : 0.013 0.116 17370 Z= 0.939 Angle : 1.652 12.309 23595 Z= 1.247 Chirality : 0.114 0.386 2733 Planarity : 0.015 0.237 2896 Dihedral : 14.120 88.325 5739 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.39 % Favored : 95.25 % Rotamer: Outliers : 1.02 % Allowed : 6.92 % Favored : 92.06 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2218 helix: -0.34 (0.12), residues: 1299 sheet: -1.86 (0.36), residues: 165 loop : -2.11 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 605 HIS 0.008 0.002 HIS G 60 PHE 0.027 0.005 PHE B 517 TYR 0.021 0.004 TYR B 440 ARG 0.011 0.002 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.15216 ( 1098) hydrogen bonds : angle 5.86738 ( 3258) SS BOND : bond 0.01430 ( 12) SS BOND : angle 2.50402 ( 24) covalent geometry : bond 0.01309 (17358) covalent geometry : angle 1.65043 (23571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 519 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9257 (mmt) cc_final: 0.8976 (mmm) REVERT: B 545 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8077 (mtm-85) REVERT: C 485 ARG cc_start: -0.0034 (mtt180) cc_final: -0.2947 (mtt90) REVERT: C 496 MET cc_start: -0.2567 (ptm) cc_final: -0.4362 (ttp) REVERT: C 813 GLU cc_start: 0.8917 (tt0) cc_final: 0.8516 (tp30) REVERT: C 817 LYS cc_start: 0.9137 (mmtp) cc_final: 0.8925 (mmtt) REVERT: D 611 ILE cc_start: 0.8199 (mm) cc_final: 0.7804 (mm) REVERT: D 803 LEU cc_start: 0.8917 (mt) cc_final: 0.8648 (mt) REVERT: E 24 MET cc_start: 0.8386 (tpt) cc_final: 0.8126 (tpp) REVERT: E 133 ASN cc_start: 0.8699 (t0) cc_final: 0.8393 (t0) REVERT: E 140 ILE cc_start: 0.9399 (mm) cc_final: 0.8860 (pt) REVERT: E 176 TYR cc_start: 0.7878 (m-80) cc_final: 0.7357 (m-80) REVERT: F 13 THR cc_start: 0.8527 (m) cc_final: 0.8327 (m) REVERT: F 84 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7887 (Cg_exo) REVERT: F 174 TYR cc_start: 0.7789 (p90) cc_final: 0.7221 (p90) REVERT: F 187 PHE cc_start: 0.7627 (t80) cc_final: 0.7218 (t80) REVERT: F 192 MET cc_start: 0.7909 (mtt) cc_final: 0.7650 (mmt) REVERT: G 76 LEU cc_start: 0.8981 (mm) cc_final: 0.8465 (mt) REVERT: G 105 SER cc_start: 0.8840 (m) cc_final: 0.8626 (p) REVERT: G 108 PRO cc_start: 0.8587 (Cg_exo) cc_final: 0.8387 (Cg_endo) REVERT: G 160 ASN cc_start: 0.8212 (m-40) cc_final: 0.7976 (m-40) REVERT: H 6 ARG cc_start: 0.7606 (tmt170) cc_final: 0.7366 (ttp80) REVERT: H 105 SER cc_start: 0.7623 (m) cc_final: 0.7235 (m) REVERT: H 125 SER cc_start: 0.9324 (t) cc_final: 0.9106 (p) REVERT: H 137 SER cc_start: 0.9180 (m) cc_final: 0.8914 (p) outliers start: 17 outliers final: 4 residues processed: 531 average time/residue: 0.3037 time to fit residues: 232.7753 Evaluate side-chains 295 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 291 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 204 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 461 ASN D 461 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 199 HIS G 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.167247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115759 restraints weight = 83310.085| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 6.73 r_work: 0.3412 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17370 Z= 0.150 Angle : 0.649 11.008 23595 Z= 0.343 Chirality : 0.043 0.183 2733 Planarity : 0.004 0.039 2896 Dihedral : 4.622 54.761 2436 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.95 % Allowed : 15.87 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.74 (0.18), residues: 2218 helix: 1.86 (0.14), residues: 1313 sheet: -1.55 (0.34), residues: 185 loop : -1.56 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 767 HIS 0.008 0.001 HIS F 60 PHE 0.025 0.001 PHE G 180 TYR 0.015 0.001 TYR A 405 ARG 0.007 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 1098) hydrogen bonds : angle 4.25907 ( 3258) SS BOND : bond 0.00592 ( 12) SS BOND : angle 1.46263 ( 24) covalent geometry : bond 0.00323 (17358) covalent geometry : angle 0.64769 (23571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TRP cc_start: 0.4894 (m100) cc_final: 0.3217 (m100) REVERT: A 496 MET cc_start: 0.7307 (ptp) cc_final: 0.6756 (ptm) REVERT: A 503 MET cc_start: 0.5887 (tmm) cc_final: 0.4912 (tmm) REVERT: B 408 MET cc_start: 0.2897 (mpp) cc_final: 0.2318 (mmm) REVERT: B 422 GLU cc_start: 0.8490 (tp30) cc_final: 0.7703 (mp0) REVERT: B 427 ASP cc_start: 0.7895 (m-30) cc_final: 0.7267 (m-30) REVERT: C 485 ARG cc_start: -0.1849 (mtt180) cc_final: -0.2985 (mtt90) REVERT: C 496 MET cc_start: 0.0628 (ptm) cc_final: -0.0882 (ttp) REVERT: C 519 ASP cc_start: 0.9284 (m-30) cc_final: 0.9053 (m-30) REVERT: C 669 LYS cc_start: 0.5626 (tptt) cc_final: 0.5163 (tppt) REVERT: C 813 GLU cc_start: 0.8924 (tt0) cc_final: 0.8473 (tp30) REVERT: D 519 ASP cc_start: 0.8217 (m-30) cc_final: 0.7717 (t70) REVERT: D 668 ASP cc_start: 0.8198 (m-30) cc_final: 0.7931 (m-30) REVERT: D 708 MET cc_start: 0.7053 (mmm) cc_final: 0.6795 (mmm) REVERT: E 24 MET cc_start: 0.8677 (tpt) cc_final: 0.8477 (tpp) REVERT: E 59 THR cc_start: 0.7373 (p) cc_final: 0.7012 (p) REVERT: E 95 GLU cc_start: 0.8001 (pt0) cc_final: 0.7719 (pm20) REVERT: E 147 LEU cc_start: 0.9373 (mm) cc_final: 0.9158 (mm) REVERT: E 174 TYR cc_start: 0.7323 (p90) cc_final: 0.6632 (p90) REVERT: E 203 ASP cc_start: 0.9298 (m-30) cc_final: 0.9068 (m-30) REVERT: F 99 ARG cc_start: 0.9237 (mtt90) cc_final: 0.8839 (tpp80) REVERT: G 10 MET cc_start: 0.8272 (ptt) cc_final: 0.7868 (ptt) REVERT: G 41 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6578 (mtmm) REVERT: G 76 LEU cc_start: 0.8640 (mm) cc_final: 0.8364 (tp) REVERT: G 127 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: H 6 ARG cc_start: 0.7928 (tmt170) cc_final: 0.7406 (ttp80) REVERT: H 10 MET cc_start: 0.8502 (tmm) cc_final: 0.8055 (tmm) REVERT: H 32 TYR cc_start: 0.7836 (m-80) cc_final: 0.7074 (m-80) REVERT: H 95 GLU cc_start: 0.8948 (tt0) cc_final: 0.8398 (tm-30) REVERT: H 180 PHE cc_start: 0.8681 (t80) cc_final: 0.8383 (t80) outliers start: 49 outliers final: 25 residues processed: 365 average time/residue: 0.2936 time to fit residues: 156.6266 Evaluate side-chains 293 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.158581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103418 restraints weight = 91139.235| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 7.58 r_work: 0.3182 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17370 Z= 0.167 Angle : 0.613 9.437 23595 Z= 0.322 Chirality : 0.042 0.211 2733 Planarity : 0.004 0.037 2896 Dihedral : 4.076 49.122 2429 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.55 % Allowed : 16.12 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2218 helix: 2.30 (0.14), residues: 1325 sheet: -1.57 (0.36), residues: 176 loop : -1.31 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 766 HIS 0.037 0.002 HIS E 199 PHE 0.015 0.001 PHE E 127 TYR 0.011 0.001 TYR C 732 ARG 0.008 0.001 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1098) hydrogen bonds : angle 4.10442 ( 3258) SS BOND : bond 0.00645 ( 12) SS BOND : angle 1.22055 ( 24) covalent geometry : bond 0.00376 (17358) covalent geometry : angle 0.61180 (23571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7347 (ptp) cc_final: 0.7041 (ptt) REVERT: A 791 ASN cc_start: 0.8649 (m110) cc_final: 0.8138 (m-40) REVERT: B 407 MET cc_start: 0.6936 (mmm) cc_final: 0.6511 (mmm) REVERT: B 408 MET cc_start: 0.2438 (mpp) cc_final: 0.1147 (mmm) REVERT: B 422 GLU cc_start: 0.8493 (tp30) cc_final: 0.7669 (pm20) REVERT: C 463 MET cc_start: 0.5644 (mpp) cc_final: 0.5128 (mpp) REVERT: C 485 ARG cc_start: -0.1676 (mtt180) cc_final: -0.3007 (mtt90) REVERT: C 496 MET cc_start: 0.0694 (ptm) cc_final: -0.0510 (tmm) REVERT: C 503 MET cc_start: -0.1884 (ttp) cc_final: -0.2100 (ttm) REVERT: C 586 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.8979 (ttm110) REVERT: C 669 LYS cc_start: 0.5849 (tptt) cc_final: 0.5161 (tmmt) REVERT: C 813 GLU cc_start: 0.9105 (tt0) cc_final: 0.8694 (tp30) REVERT: D 420 ARG cc_start: 0.4178 (OUTLIER) cc_final: 0.3212 (mmm160) REVERT: D 519 ASP cc_start: 0.8878 (m-30) cc_final: 0.8346 (t70) REVERT: D 524 GLU cc_start: 0.8764 (mp0) cc_final: 0.8515 (mp0) REVERT: D 529 ILE cc_start: 0.9498 (mt) cc_final: 0.9298 (mt) REVERT: D 668 ASP cc_start: 0.8223 (m-30) cc_final: 0.7942 (m-30) REVERT: D 670 MET cc_start: 0.5845 (tpp) cc_final: 0.5375 (tpt) REVERT: E 13 THR cc_start: 0.9122 (m) cc_final: 0.8839 (m) REVERT: E 101 VAL cc_start: 0.9388 (t) cc_final: 0.9171 (p) REVERT: F 174 TYR cc_start: 0.8535 (p90) cc_final: 0.8047 (p90) REVERT: G 24 MET cc_start: 0.8790 (tpt) cc_final: 0.7802 (tpt) REVERT: G 41 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6694 (ptpp) REVERT: G 76 LEU cc_start: 0.8905 (mm) cc_final: 0.8460 (tp) REVERT: G 127 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: H 6 ARG cc_start: 0.8096 (tmt170) cc_final: 0.7656 (ttp80) REVERT: H 10 MET cc_start: 0.8554 (tmm) cc_final: 0.8161 (tmm) REVERT: H 13 THR cc_start: 0.9037 (m) cc_final: 0.8791 (t) REVERT: H 95 GLU cc_start: 0.9074 (tt0) cc_final: 0.8459 (tm-30) outliers start: 59 outliers final: 32 residues processed: 311 average time/residue: 0.3010 time to fit residues: 139.6522 Evaluate side-chains 274 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 97 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 200 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 36 optimal weight: 0.7980 chunk 158 optimal weight: 0.2980 chunk 224 optimal weight: 3.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.154514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101824 restraints weight = 73066.076| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 7.92 r_work: 0.3091 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17370 Z= 0.181 Angle : 0.606 8.501 23595 Z= 0.319 Chirality : 0.042 0.172 2733 Planarity : 0.004 0.038 2896 Dihedral : 3.880 34.738 2427 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.73 % Allowed : 17.44 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2218 helix: 2.48 (0.14), residues: 1318 sheet: -1.56 (0.39), residues: 166 loop : -1.18 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 671 HIS 0.016 0.001 HIS E 199 PHE 0.032 0.002 PHE C 659 TYR 0.019 0.001 TYR D 647 ARG 0.007 0.001 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 1098) hydrogen bonds : angle 4.03809 ( 3258) SS BOND : bond 0.00540 ( 12) SS BOND : angle 1.36122 ( 24) covalent geometry : bond 0.00418 (17358) covalent geometry : angle 0.60434 (23571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 THR cc_start: 0.5837 (OUTLIER) cc_final: 0.5134 (t) REVERT: B 407 MET cc_start: 0.6464 (mmm) cc_final: 0.6205 (mmm) REVERT: B 408 MET cc_start: 0.2551 (mpp) cc_final: 0.2306 (mmm) REVERT: C 485 ARG cc_start: -0.1901 (mtt180) cc_final: -0.3005 (mtt90) REVERT: C 496 MET cc_start: 0.1662 (ptm) cc_final: 0.0736 (ttp) REVERT: C 586 ARG cc_start: 0.9272 (mmm-85) cc_final: 0.9012 (ttm110) REVERT: C 813 GLU cc_start: 0.9166 (tt0) cc_final: 0.8833 (tp30) REVERT: D 503 MET cc_start: 0.7105 (tmm) cc_final: 0.6736 (tmm) REVERT: D 519 ASP cc_start: 0.9217 (m-30) cc_final: 0.8739 (t70) REVERT: D 524 GLU cc_start: 0.9145 (mp0) cc_final: 0.8850 (mp0) REVERT: D 668 ASP cc_start: 0.8404 (m-30) cc_final: 0.8126 (m-30) REVERT: E 56 GLU cc_start: 0.7128 (tt0) cc_final: 0.6847 (tm-30) REVERT: E 61 SER cc_start: 0.9131 (t) cc_final: 0.8908 (p) REVERT: E 101 VAL cc_start: 0.9555 (t) cc_final: 0.9333 (p) REVERT: E 191 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8983 (mm-30) REVERT: E 205 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: F 70 GLU cc_start: 0.7453 (mp0) cc_final: 0.6897 (pp20) REVERT: G 6 ARG cc_start: 0.7525 (tpt90) cc_final: 0.7235 (tpt90) REVERT: G 10 MET cc_start: 0.8398 (ptt) cc_final: 0.8083 (ptt) REVERT: G 24 MET cc_start: 0.8930 (tpt) cc_final: 0.8053 (tpt) REVERT: G 41 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.5712 (mtmm) REVERT: G 58 MET cc_start: 0.8095 (mmm) cc_final: 0.7815 (tpp) REVERT: G 76 LEU cc_start: 0.8949 (mm) cc_final: 0.8550 (tp) REVERT: G 185 LEU cc_start: 0.9437 (tt) cc_final: 0.9195 (tp) REVERT: H 6 ARG cc_start: 0.8303 (tmt170) cc_final: 0.7974 (ttp80) REVERT: H 10 MET cc_start: 0.8451 (tmm) cc_final: 0.8220 (tmm) REVERT: H 95 GLU cc_start: 0.9103 (tt0) cc_final: 0.8470 (tm-30) outliers start: 62 outliers final: 41 residues processed: 288 average time/residue: 0.3080 time to fit residues: 130.2404 Evaluate side-chains 269 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 206 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.147661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089411 restraints weight = 110370.645| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 8.67 r_work: 0.2923 rms_B_bonded: 6.64 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17370 Z= 0.274 Angle : 0.686 8.390 23595 Z= 0.363 Chirality : 0.044 0.196 2733 Planarity : 0.004 0.053 2896 Dihedral : 4.200 37.355 2427 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.81 % Allowed : 18.46 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2218 helix: 2.18 (0.14), residues: 1321 sheet: -1.43 (0.43), residues: 135 loop : -1.18 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 671 HIS 0.007 0.002 HIS D 435 PHE 0.021 0.002 PHE D 607 TYR 0.032 0.002 TYR D 647 ARG 0.027 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1098) hydrogen bonds : angle 4.31350 ( 3258) SS BOND : bond 0.01161 ( 12) SS BOND : angle 1.41030 ( 24) covalent geometry : bond 0.00631 (17358) covalent geometry : angle 0.68532 (23571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7853 (ptm) cc_final: 0.7161 (ppp) REVERT: A 502 ILE cc_start: 0.8013 (mt) cc_final: 0.7781 (mt) REVERT: A 721 MET cc_start: 0.7944 (mtm) cc_final: 0.7705 (mtm) REVERT: A 722 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.6927 (ttmm) REVERT: B 407 MET cc_start: 0.6460 (mmm) cc_final: 0.6179 (mmm) REVERT: B 408 MET cc_start: 0.1416 (mpp) cc_final: 0.1205 (mmm) REVERT: B 619 ASN cc_start: 0.9649 (t0) cc_final: 0.9426 (t0) REVERT: C 463 MET cc_start: 0.5694 (mpp) cc_final: 0.5435 (mpp) REVERT: C 485 ARG cc_start: -0.1521 (mtt180) cc_final: -0.2938 (mtt90) REVERT: C 669 LYS cc_start: 0.5903 (tptt) cc_final: 0.5686 (tppt) REVERT: C 674 MET cc_start: 0.2458 (mtt) cc_final: 0.2131 (mpp) REVERT: C 813 GLU cc_start: 0.9256 (tt0) cc_final: 0.9045 (tp30) REVERT: D 473 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7660 (p0) REVERT: D 519 ASP cc_start: 0.9395 (m-30) cc_final: 0.8955 (t70) REVERT: D 586 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.9235 (mmm-85) REVERT: D 668 ASP cc_start: 0.8486 (m-30) cc_final: 0.8230 (m-30) REVERT: E 205 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8064 (t-90) REVERT: F 24 MET cc_start: 0.9351 (tpt) cc_final: 0.9034 (tpt) REVERT: F 37 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7155 (ptt-90) REVERT: F 70 GLU cc_start: 0.8056 (mp0) cc_final: 0.7210 (pp20) REVERT: F 128 TYR cc_start: 0.8381 (t80) cc_final: 0.7587 (t80) REVERT: G 6 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7484 (tpt90) REVERT: G 10 MET cc_start: 0.8330 (ptt) cc_final: 0.8110 (ptt) REVERT: G 13 THR cc_start: 0.9261 (t) cc_final: 0.8971 (p) REVERT: G 41 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6670 (ptpp) REVERT: G 76 LEU cc_start: 0.9086 (mm) cc_final: 0.8814 (tp) REVERT: G 117 MET cc_start: 0.9219 (mmp) cc_final: 0.8643 (mtt) REVERT: G 185 LEU cc_start: 0.9477 (tt) cc_final: 0.9235 (tp) REVERT: H 6 ARG cc_start: 0.8464 (tmt170) cc_final: 0.8214 (tmm160) REVERT: H 109 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9163 (pt) REVERT: H 199 HIS cc_start: 0.9501 (OUTLIER) cc_final: 0.9117 (t-170) outliers start: 80 outliers final: 56 residues processed: 288 average time/residue: 0.3236 time to fit residues: 135.1683 Evaluate side-chains 273 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 39 VAL 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 150 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 220 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** 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 = 0.4366 r_free = 0.4366 target = 0.149185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094383 restraints weight = 90278.487| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 8.20 r_work: 0.2986 rms_B_bonded: 6.44 restraints_weight: 2.0000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17370 Z= 0.143 Angle : 0.589 9.982 23595 Z= 0.304 Chirality : 0.041 0.187 2733 Planarity : 0.003 0.043 2896 Dihedral : 3.837 19.840 2425 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.95 % Allowed : 20.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2218 helix: 2.58 (0.14), residues: 1318 sheet: -1.24 (0.43), residues: 140 loop : -1.11 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 671 HIS 0.004 0.001 HIS D 412 PHE 0.030 0.001 PHE F 73 TYR 0.015 0.001 TYR D 732 ARG 0.010 0.001 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1098) hydrogen bonds : angle 3.97995 ( 3258) SS BOND : bond 0.00416 ( 12) SS BOND : angle 1.32544 ( 24) covalent geometry : bond 0.00328 (17358) covalent geometry : angle 0.58739 (23571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7917 (ptm) cc_final: 0.7458 (ppp) REVERT: B 674 MET cc_start: 0.1699 (ptp) cc_final: 0.1451 (ptm) REVERT: C 463 MET cc_start: 0.5321 (mpp) cc_final: 0.5047 (mpp) REVERT: C 485 ARG cc_start: -0.1917 (mtt180) cc_final: -0.3316 (mtt90) REVERT: C 496 MET cc_start: -0.0518 (ptm) cc_final: -0.0863 (tmm) REVERT: C 669 LYS cc_start: 0.5772 (tptt) cc_final: 0.5380 (tppt) REVERT: C 674 MET cc_start: 0.2430 (mtt) cc_final: 0.2112 (mpp) REVERT: C 813 GLU cc_start: 0.9196 (tt0) cc_final: 0.8983 (tp30) REVERT: D 473 ASP cc_start: 0.8177 (m-30) cc_final: 0.7586 (p0) REVERT: D 503 MET cc_start: 0.7689 (tmm) cc_final: 0.7348 (tmm) REVERT: D 519 ASP cc_start: 0.9348 (m-30) cc_final: 0.8894 (t70) REVERT: D 668 ASP cc_start: 0.8431 (m-30) cc_final: 0.8148 (m-30) REVERT: D 721 MET cc_start: 0.8016 (ppp) cc_final: 0.7596 (ppp) REVERT: E 101 VAL cc_start: 0.9439 (t) cc_final: 0.9050 (p) REVERT: E 191 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9094 (mm-30) REVERT: E 205 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8092 (t-90) REVERT: F 37 ARG cc_start: 0.7262 (ttm170) cc_final: 0.6877 (ptt-90) REVERT: F 70 GLU cc_start: 0.8094 (mp0) cc_final: 0.7248 (pp20) REVERT: F 72 ASN cc_start: 0.7785 (p0) cc_final: 0.7502 (p0) REVERT: F 128 TYR cc_start: 0.8388 (t80) cc_final: 0.7710 (t80) REVERT: G 6 ARG cc_start: 0.7634 (tpt90) cc_final: 0.7357 (tpt90) REVERT: G 10 MET cc_start: 0.8263 (ptt) cc_final: 0.8010 (ptt) REVERT: G 13 THR cc_start: 0.9183 (t) cc_final: 0.8963 (p) REVERT: G 41 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6485 (ptpp) REVERT: G 72 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7823 (p0) REVERT: G 76 LEU cc_start: 0.9070 (mm) cc_final: 0.8783 (tp) REVERT: G 185 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9124 (tt) REVERT: H 58 MET cc_start: 0.9009 (tpt) cc_final: 0.8485 (tpt) REVERT: H 95 GLU cc_start: 0.9058 (tt0) cc_final: 0.8792 (pp20) REVERT: H 109 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9029 (pt) REVERT: H 199 HIS cc_start: 0.9297 (OUTLIER) cc_final: 0.9050 (t-170) outliers start: 49 outliers final: 33 residues processed: 281 average time/residue: 0.3118 time to fit residues: 127.5202 Evaluate side-chains 261 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 165 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 106 optimal weight: 40.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 132 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090984 restraints weight = 67515.493| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 6.38 r_work: 0.2990 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17370 Z= 0.243 Angle : 0.664 10.779 23595 Z= 0.345 Chirality : 0.043 0.214 2733 Planarity : 0.004 0.044 2896 Dihedral : 3.948 18.995 2425 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.27 % Allowed : 20.51 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2218 helix: 2.38 (0.14), residues: 1317 sheet: -1.29 (0.44), residues: 139 loop : -1.05 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 766 HIS 0.005 0.001 HIS H 199 PHE 0.023 0.002 PHE F 73 TYR 0.021 0.002 TYR A 424 ARG 0.012 0.001 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1098) hydrogen bonds : angle 4.20885 ( 3258) SS BOND : bond 0.00606 ( 12) SS BOND : angle 1.81492 ( 24) covalent geometry : bond 0.00563 (17358) covalent geometry : angle 0.66195 (23571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8393 (ptm) cc_final: 0.7598 (ppp) REVERT: A 674 MET cc_start: 0.7420 (ptp) cc_final: 0.7129 (ptt) REVERT: C 485 ARG cc_start: -0.1421 (mtt180) cc_final: -0.3077 (mtt90) REVERT: C 496 MET cc_start: -0.0066 (ptm) cc_final: -0.0461 (tmm) REVERT: C 674 MET cc_start: 0.2576 (mtt) cc_final: 0.2204 (mpp) REVERT: C 813 GLU cc_start: 0.9157 (tt0) cc_final: 0.8940 (mm-30) REVERT: D 407 MET cc_start: 0.4089 (ptt) cc_final: 0.3768 (pmm) REVERT: D 473 ASP cc_start: 0.8200 (m-30) cc_final: 0.7562 (p0) REVERT: D 503 MET cc_start: 0.7840 (tmm) cc_final: 0.7562 (tmm) REVERT: D 519 ASP cc_start: 0.9329 (m-30) cc_final: 0.8901 (t70) REVERT: D 586 ARG cc_start: 0.9424 (mmm-85) cc_final: 0.9123 (mmm-85) REVERT: D 668 ASP cc_start: 0.8124 (m-30) cc_final: 0.7870 (m-30) REVERT: D 721 MET cc_start: 0.7874 (ppp) cc_final: 0.7509 (ppp) REVERT: E 58 MET cc_start: 0.8556 (tpt) cc_final: 0.8300 (tpt) REVERT: E 191 GLU cc_start: 0.9268 (mm-30) cc_final: 0.9011 (mm-30) REVERT: E 205 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8055 (t-90) REVERT: F 128 TYR cc_start: 0.8357 (t80) cc_final: 0.7498 (t80) REVERT: F 207 GLN cc_start: 0.9051 (pt0) cc_final: 0.8822 (pp30) REVERT: G 6 ARG cc_start: 0.7522 (tpt90) cc_final: 0.7149 (tpt90) REVERT: G 13 THR cc_start: 0.9222 (t) cc_final: 0.8958 (p) REVERT: G 117 MET cc_start: 0.9243 (mmp) cc_final: 0.8802 (mtp) REVERT: G 185 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9165 (tp) REVERT: H 6 ARG cc_start: 0.8567 (tmm160) cc_final: 0.7609 (ttp80) REVERT: H 109 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9034 (pt) REVERT: H 199 HIS cc_start: 0.9364 (OUTLIER) cc_final: 0.8998 (t-170) outliers start: 71 outliers final: 44 residues processed: 261 average time/residue: 0.3314 time to fit residues: 126.3209 Evaluate side-chains 256 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 171 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 193 optimal weight: 0.1980 chunk 206 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096019 restraints weight = 88569.733| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 7.79 r_work: 0.3028 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17370 Z= 0.118 Angle : 0.627 12.536 23595 Z= 0.318 Chirality : 0.041 0.296 2733 Planarity : 0.003 0.044 2896 Dihedral : 3.855 23.321 2425 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.77 % Allowed : 22.31 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2218 helix: 2.68 (0.14), residues: 1318 sheet: -0.93 (0.45), residues: 142 loop : -0.95 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.005 0.001 HIS F 60 PHE 0.022 0.001 PHE F 73 TYR 0.015 0.001 TYR A 424 ARG 0.011 0.001 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1098) hydrogen bonds : angle 3.88476 ( 3258) SS BOND : bond 0.00717 ( 12) SS BOND : angle 2.89508 ( 24) covalent geometry : bond 0.00253 (17358) covalent geometry : angle 0.62064 (23571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8101 (ptm) cc_final: 0.7518 (ppp) REVERT: B 674 MET cc_start: 0.2093 (ptp) cc_final: 0.1884 (ptm) REVERT: C 463 MET cc_start: 0.5346 (mpp) cc_final: 0.5115 (mpp) REVERT: C 485 ARG cc_start: -0.1565 (mtt180) cc_final: -0.3078 (mtt90) REVERT: C 496 MET cc_start: -0.0190 (ptm) cc_final: -0.0609 (tmm) REVERT: C 586 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.9001 (ttm-80) REVERT: C 669 LYS cc_start: 0.5805 (tptt) cc_final: 0.5460 (tppt) REVERT: C 674 MET cc_start: 0.2439 (mtt) cc_final: 0.2151 (mpp) REVERT: D 408 MET cc_start: 0.6344 (tpt) cc_final: 0.6124 (tpt) REVERT: D 473 ASP cc_start: 0.8084 (m-30) cc_final: 0.7443 (p0) REVERT: D 503 MET cc_start: 0.7846 (tmm) cc_final: 0.7441 (tmm) REVERT: D 519 ASP cc_start: 0.9327 (m-30) cc_final: 0.8833 (t70) REVERT: D 668 ASP cc_start: 0.8364 (m-30) cc_final: 0.8130 (m-30) REVERT: D 721 MET cc_start: 0.7809 (ppp) cc_final: 0.7586 (ppp) REVERT: E 18 PHE cc_start: 0.9424 (t80) cc_final: 0.9170 (t80) REVERT: E 58 MET cc_start: 0.8710 (tpt) cc_final: 0.8479 (tpt) REVERT: E 65 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8264 (ptp-170) REVERT: E 191 GLU cc_start: 0.9243 (mm-30) cc_final: 0.9013 (mm-30) REVERT: E 205 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8265 (t-90) REVERT: F 128 TYR cc_start: 0.8346 (t80) cc_final: 0.7418 (t80) REVERT: G 6 ARG cc_start: 0.7506 (tpt90) cc_final: 0.7073 (tpt90) REVERT: G 13 THR cc_start: 0.9145 (t) cc_final: 0.8917 (p) REVERT: G 185 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9122 (tt) REVERT: H 95 GLU cc_start: 0.8970 (tt0) cc_final: 0.8578 (pp20) REVERT: H 97 PHE cc_start: 0.8990 (t80) cc_final: 0.8735 (t80) REVERT: H 109 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8894 (pt) REVERT: H 192 MET cc_start: 0.9119 (mtm) cc_final: 0.8715 (mmt) outliers start: 46 outliers final: 26 residues processed: 279 average time/residue: 0.3030 time to fit residues: 126.0181 Evaluate side-chains 255 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** 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 = 0.4311 r_free = 0.4311 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089887 restraints weight = 71062.454| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 6.42 r_work: 0.2979 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17370 Z= 0.240 Angle : 0.707 12.530 23595 Z= 0.364 Chirality : 0.043 0.189 2733 Planarity : 0.004 0.044 2896 Dihedral : 4.028 30.346 2425 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.47 % Allowed : 22.91 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2218 helix: 2.41 (0.14), residues: 1318 sheet: -1.26 (0.48), residues: 124 loop : -0.92 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 766 HIS 0.012 0.001 HIS E 199 PHE 0.030 0.002 PHE H 127 TYR 0.015 0.002 TYR D 549 ARG 0.010 0.001 ARG G 6 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1098) hydrogen bonds : angle 4.21129 ( 3258) SS BOND : bond 0.00419 ( 12) SS BOND : angle 1.95359 ( 24) covalent geometry : bond 0.00556 (17358) covalent geometry : angle 0.70483 (23571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8301 (ptm) cc_final: 0.7666 (ppp) REVERT: C 485 ARG cc_start: -0.1395 (mtt180) cc_final: -0.3033 (mtt90) REVERT: C 496 MET cc_start: -0.0672 (ptm) cc_final: -0.1091 (tmm) REVERT: C 524 GLU cc_start: 0.9095 (mp0) cc_final: 0.8856 (mp0) REVERT: C 647 TYR cc_start: 0.4302 (p90) cc_final: 0.2822 (p90) REVERT: C 669 LYS cc_start: 0.5657 (tptt) cc_final: 0.5235 (tptt) REVERT: C 708 MET cc_start: 0.5550 (tpp) cc_final: 0.5312 (ptp) REVERT: D 473 ASP cc_start: 0.8324 (m-30) cc_final: 0.7612 (p0) REVERT: D 519 ASP cc_start: 0.9295 (m-30) cc_final: 0.8889 (t70) REVERT: D 586 ARG cc_start: 0.9390 (mmm-85) cc_final: 0.9093 (mmm-85) REVERT: D 668 ASP cc_start: 0.8046 (m-30) cc_final: 0.7785 (m-30) REVERT: E 58 MET cc_start: 0.8518 (tpt) cc_final: 0.8300 (tpt) REVERT: E 191 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9044 (mm-30) REVERT: E 205 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.8199 (t-90) REVERT: F 128 TYR cc_start: 0.8136 (t80) cc_final: 0.7259 (t80) REVERT: G 13 THR cc_start: 0.9223 (t) cc_final: 0.8965 (p) REVERT: G 185 LEU cc_start: 0.9426 (tt) cc_final: 0.9162 (tp) REVERT: H 6 ARG cc_start: 0.8905 (tmm160) cc_final: 0.8253 (tmm160) REVERT: H 97 PHE cc_start: 0.9048 (t80) cc_final: 0.8714 (t80) REVERT: H 109 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.8994 (pt) outliers start: 41 outliers final: 34 residues processed: 245 average time/residue: 0.3145 time to fit residues: 112.9759 Evaluate side-chains 244 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 149 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.143571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086078 restraints weight = 62728.019| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 5.52 r_work: 0.2998 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.8571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17370 Z= 0.241 Angle : 0.697 12.957 23595 Z= 0.358 Chirality : 0.043 0.262 2733 Planarity : 0.004 0.089 2896 Dihedral : 4.067 30.219 2425 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.83 % Allowed : 22.67 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2218 helix: 2.41 (0.14), residues: 1316 sheet: -1.11 (0.47), residues: 135 loop : -0.93 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 460 HIS 0.009 0.002 HIS H 60 PHE 0.026 0.002 PHE H 127 TYR 0.013 0.001 TYR B 797 ARG 0.011 0.001 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1098) hydrogen bonds : angle 4.18205 ( 3258) SS BOND : bond 0.00452 ( 12) SS BOND : angle 1.80991 ( 24) covalent geometry : bond 0.00555 (17358) covalent geometry : angle 0.69465 (23571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7887 (ptm) cc_final: 0.7184 (ppp) REVERT: B 668 ASP cc_start: 0.7811 (t0) cc_final: 0.7558 (m-30) REVERT: C 463 MET cc_start: 0.5884 (mpp) cc_final: 0.5650 (mpp) REVERT: C 496 MET cc_start: -0.0256 (ptm) cc_final: -0.0674 (tmm) REVERT: C 524 GLU cc_start: 0.9054 (mp0) cc_final: 0.8845 (mp0) REVERT: C 669 LYS cc_start: 0.5927 (tptt) cc_final: 0.5478 (tppt) REVERT: D 473 ASP cc_start: 0.8241 (m-30) cc_final: 0.7458 (p0) REVERT: D 503 MET cc_start: 0.7352 (tmm) cc_final: 0.7072 (tmm) REVERT: D 519 ASP cc_start: 0.9256 (m-30) cc_final: 0.8855 (t70) REVERT: D 586 ARG cc_start: 0.9378 (mmm-85) cc_final: 0.9097 (mmm-85) REVERT: E 58 MET cc_start: 0.8503 (tpt) cc_final: 0.8269 (tpt) REVERT: E 191 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9024 (mm-30) REVERT: E 205 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8116 (t-90) REVERT: F 128 TYR cc_start: 0.8195 (t80) cc_final: 0.7222 (t80) REVERT: G 92 ASP cc_start: 0.8393 (t0) cc_final: 0.6398 (t0) REVERT: G 95 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8746 (pt0) REVERT: G 117 MET cc_start: 0.9205 (mmp) cc_final: 0.8652 (mtt) REVERT: G 185 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9199 (tp) REVERT: H 6 ARG cc_start: 0.8944 (tmm160) cc_final: 0.8378 (tmm160) REVERT: H 97 PHE cc_start: 0.9037 (t80) cc_final: 0.8776 (t80) REVERT: H 109 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9055 (pt) REVERT: H 199 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.9022 (t-170) outliers start: 47 outliers final: 39 residues processed: 245 average time/residue: 0.2937 time to fit residues: 106.4549 Evaluate side-chains 246 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 67 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.144251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090857 restraints weight = 90560.930| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 7.51 r_work: 0.2943 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17370 Z= 0.184 Angle : 0.670 12.783 23595 Z= 0.342 Chirality : 0.042 0.184 2733 Planarity : 0.004 0.048 2896 Dihedral : 4.018 29.547 2425 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 23.45 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2218 helix: 2.47 (0.14), residues: 1319 sheet: -0.95 (0.45), residues: 148 loop : -0.95 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 460 HIS 0.023 0.001 HIS E 199 PHE 0.027 0.002 PHE F 97 TYR 0.016 0.001 TYR A 440 ARG 0.010 0.001 ARG G 6 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1098) hydrogen bonds : angle 4.08836 ( 3258) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.52550 ( 24) covalent geometry : bond 0.00425 (17358) covalent geometry : angle 0.66825 (23571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11155.30 seconds wall clock time: 192 minutes 35.29 seconds (11555.29 seconds total)