Starting phenix.real_space_refine on Sun Aug 24 04:23:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3z_17400/08_2025/8p3z_17400.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3z_17400/08_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_17400/08_2025/8p3z_17400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3z_17400/08_2025/8p3z_17400.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3z_17400/08_2025/8p3z_17400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3z_17400/08_2025/8p3z_17400.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'ARG:plan': 6, 'GLN:plan1': 2, 'TYR:plan': 1} 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: {'GLU:plan': 12, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'GLU:plan': 12, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1} 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: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1} 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: {'GLU:plan': 14, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: 5.36, per 1000 atoms: 0.32 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: 1.53 Conformation dependent library (CDL) restraints added in 947.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.48 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: 2.87 Time building geometry restraints manager: 2.03 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.570 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- 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 : 8.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.002 ARG F 99 TYR 0.021 0.004 TYR B 440 PHE 0.027 0.005 PHE B 517 TRP 0.025 0.005 TRP B 605 HIS 0.008 0.002 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.01309 (17358) covalent geometry : angle 1.65043 (23571) SS BOND : bond 0.01430 ( 12) SS BOND : angle 2.50402 ( 24) hydrogen bonds : bond 0.15216 ( 1098) hydrogen bonds : angle 5.86738 ( 3258) *********************** 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 : 0.526 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: 0.8078 (mtm-85) REVERT: C 485 ARG cc_start: -0.0034 (mtt180) cc_final: -0.2945 (mmt90) REVERT: C 496 MET cc_start: -0.2567 (ptm) cc_final: -0.4359 (ttp) REVERT: C 813 GLU cc_start: 0.8917 (tt0) cc_final: 0.8518 (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: 0.8127 (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: 0.8861 (pt) REVERT: E 176 TYR cc_start: 0.7878 (m-80) cc_final: 0.7358 (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: 0.7889 (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: 0.7651 (mmt) REVERT: G 76 LEU cc_start: 0.8981 (mm) cc_final: 0.8466 (mt) REVERT: G 105 SER cc_start: 0.8840 (m) cc_final: 0.8624 (p) REVERT: G 160 ASN cc_start: 0.8212 (m-40) cc_final: 0.7973 (m-40) REVERT: H 6 ARG cc_start: 0.7606 (tmt170) cc_final: 0.7368 (ttp80) REVERT: H 105 SER cc_start: 0.7623 (m) cc_final: 0.7234 (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: 3 residues processed: 531 average time/residue: 0.1403 time to fit residues: 108.3161 Evaluate side-chains 291 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.0270 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 F 207 GLN G 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.166979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117688 restraints weight = 63698.693| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 7.22 r_work: 0.3429 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17370 Z= 0.146 Angle : 0.652 11.692 23595 Z= 0.343 Chirality : 0.043 0.180 2733 Planarity : 0.004 0.043 2896 Dihedral : 4.555 55.694 2432 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.89 % Allowed : 15.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2218 helix: 1.82 (0.14), residues: 1312 sheet: -1.55 (0.34), residues: 185 loop : -1.58 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 65 TYR 0.015 0.001 TYR A 405 PHE 0.026 0.002 PHE G 180 TRP 0.014 0.001 TRP C 766 HIS 0.008 0.002 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00308 (17358) covalent geometry : angle 0.65034 (23571) SS BOND : bond 0.00441 ( 12) SS BOND : angle 1.50062 ( 24) hydrogen bonds : bond 0.04689 ( 1098) hydrogen bonds : angle 4.23755 ( 3258) *********************** 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 388 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 0.789 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: 0.4661 (m100) cc_final: 0.3588 (m100) REVERT: A 496 MET cc_start: 0.7341 (ptp) cc_final: 0.6736 (ptp) REVERT: B 408 MET cc_start: 0.2668 (mpp) cc_final: 0.2167 (mmm) REVERT: B 422 GLU cc_start: 0.8463 (tp30) cc_final: 0.7664 (mp0) REVERT: B 427 ASP cc_start: 0.7846 (m-30) cc_final: 0.7222 (m-30) REVERT: C 485 ARG cc_start: -0.1894 (mtt180) cc_final: -0.2990 (mtt90) REVERT: C 496 MET cc_start: 0.0135 (ptm) cc_final: -0.1399 (ttp) REVERT: C 519 ASP cc_start: 0.9239 (m-30) cc_final: 0.9002 (m-30) REVERT: C 669 LYS cc_start: 0.5722 (tptt) cc_final: 0.5280 (tppt) REVERT: C 813 GLU cc_start: 0.8823 (tt0) cc_final: 0.8380 (tp30) REVERT: D 420 ARG cc_start: 0.3208 (OUTLIER) cc_final: 0.1873 (mmm160) REVERT: D 519 ASP cc_start: 0.8105 (m-30) cc_final: 0.7654 (t70) REVERT: D 668 ASP cc_start: 0.8201 (m-30) cc_final: 0.7943 (m-30) REVERT: E 24 MET cc_start: 0.8632 (tpt) cc_final: 0.8305 (tpp) REVERT: E 59 THR cc_start: 0.7443 (p) cc_final: 0.7065 (p) REVERT: E 95 GLU cc_start: 0.7988 (pt0) cc_final: 0.7718 (pm20) REVERT: E 174 TYR cc_start: 0.7300 (p90) cc_final: 0.6605 (p90) REVERT: E 203 ASP cc_start: 0.9251 (m-30) cc_final: 0.9017 (m-30) REVERT: G 41 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6579 (mtmm) REVERT: G 76 LEU cc_start: 0.8621 (mm) cc_final: 0.8343 (tp) REVERT: G 127 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: H 6 ARG cc_start: 0.7861 (tmt170) cc_final: 0.7532 (ttp80) REVERT: H 10 MET cc_start: 0.8502 (tmm) cc_final: 0.8041 (tmm) REVERT: H 32 TYR cc_start: 0.7792 (m-80) cc_final: 0.6971 (m-80) REVERT: H 95 GLU cc_start: 0.8874 (tt0) cc_final: 0.8293 (tm-30) REVERT: H 180 PHE cc_start: 0.8768 (t80) cc_final: 0.8469 (t80) outliers start: 48 outliers final: 24 residues processed: 365 average time/residue: 0.1466 time to fit residues: 79.0325 Evaluate side-chains 297 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 28 VAL 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 166 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN ** 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 = 0.4459 r_free = 0.4459 target = 0.158884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102592 restraints weight = 95601.284| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 7.90 r_work: 0.3178 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17370 Z= 0.166 Angle : 0.603 8.425 23595 Z= 0.317 Chirality : 0.042 0.215 2733 Planarity : 0.004 0.036 2896 Dihedral : 4.116 49.529 2429 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.07 % Allowed : 16.96 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2218 helix: 2.30 (0.14), residues: 1325 sheet: -1.46 (0.38), residues: 163 loop : -1.40 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 453 TYR 0.011 0.001 TYR C 732 PHE 0.021 0.001 PHE E 127 TRP 0.014 0.001 TRP D 767 HIS 0.038 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00378 (17358) covalent geometry : angle 0.60213 (23571) SS BOND : bond 0.00372 ( 12) SS BOND : angle 1.23168 ( 24) hydrogen bonds : bond 0.04113 ( 1098) hydrogen bonds : angle 4.14003 ( 3258) *********************** 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 320 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.440 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 721 MET cc_start: 0.8050 (mtt) cc_final: 0.7676 (mtm) REVERT: A 791 ASN cc_start: 0.8572 (m110) cc_final: 0.8201 (m-40) REVERT: B 407 MET cc_start: 0.6996 (mmm) cc_final: 0.6685 (mmm) REVERT: B 408 MET cc_start: 0.2517 (mpp) cc_final: 0.2264 (mmm) REVERT: C 463 MET cc_start: 0.5665 (mpp) cc_final: 0.5166 (mpp) REVERT: C 485 ARG cc_start: -0.1648 (mtt180) cc_final: -0.3004 (mtt90) REVERT: C 496 MET cc_start: 0.0562 (ptm) cc_final: -0.0667 (tmm) REVERT: C 669 LYS cc_start: 0.5840 (tptt) cc_final: 0.5136 (tmmt) REVERT: C 813 GLU cc_start: 0.9111 (tt0) cc_final: 0.8693 (tp30) REVERT: D 519 ASP cc_start: 0.8904 (m-30) cc_final: 0.8402 (t70) REVERT: D 524 GLU cc_start: 0.8755 (mp0) cc_final: 0.8474 (mp0) REVERT: D 668 ASP cc_start: 0.8297 (m-30) cc_final: 0.8051 (m-30) REVERT: E 13 THR cc_start: 0.9110 (m) cc_final: 0.8827 (m) REVERT: E 147 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9304 (mt) REVERT: E 205 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7422 (t-90) REVERT: F 174 TYR cc_start: 0.8539 (p90) cc_final: 0.8044 (p90) REVERT: G 24 MET cc_start: 0.8843 (tpt) cc_final: 0.7825 (tpt) REVERT: G 41 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6575 (ptpp) REVERT: G 76 LEU cc_start: 0.8867 (mm) cc_final: 0.8441 (tp) REVERT: G 127 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: H 6 ARG cc_start: 0.8297 (tmt170) cc_final: 0.7701 (ttp80) REVERT: H 10 MET cc_start: 0.8576 (tmm) cc_final: 0.8170 (tmm) REVERT: H 13 THR cc_start: 0.8960 (m) cc_final: 0.8721 (t) REVERT: H 95 GLU cc_start: 0.9079 (tt0) cc_final: 0.8458 (tm-30) outliers start: 51 outliers final: 29 residues processed: 308 average time/residue: 0.1261 time to fit residues: 58.0825 Evaluate side-chains 274 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 591 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 597 SER 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 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 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 147 LEU 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 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 57 VAL Chi-restraints excluded: chain F residue 150 ILE 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 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 166 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 E 199 HIS F 207 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.158082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102623 restraints weight = 80747.046| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 6.67 r_work: 0.3187 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17370 Z= 0.126 Angle : 0.564 8.302 23595 Z= 0.295 Chirality : 0.041 0.170 2733 Planarity : 0.003 0.037 2896 Dihedral : 3.847 37.509 2427 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.07 % Allowed : 17.98 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.18), residues: 2218 helix: 2.52 (0.14), residues: 1325 sheet: -1.14 (0.38), residues: 158 loop : -1.28 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 586 TYR 0.010 0.001 TYR A 732 PHE 0.020 0.001 PHE D 607 TRP 0.030 0.001 TRP C 671 HIS 0.009 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00284 (17358) covalent geometry : angle 0.56320 (23571) SS BOND : bond 0.00526 ( 12) SS BOND : angle 1.18909 ( 24) hydrogen bonds : bond 0.03684 ( 1098) hydrogen bonds : angle 3.95645 ( 3258) *********************** 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 311 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7161 (ptm) cc_final: 0.5773 (ppp) REVERT: A 721 MET cc_start: 0.8113 (mtt) cc_final: 0.7794 (mtm) REVERT: A 791 ASN cc_start: 0.8882 (m110) cc_final: 0.8527 (m-40) REVERT: B 407 MET cc_start: 0.6664 (mmm) cc_final: 0.6202 (mmm) REVERT: B 408 MET cc_start: 0.2351 (mpp) cc_final: 0.1013 (mmm) REVERT: B 422 GLU cc_start: 0.8455 (tp30) cc_final: 0.7614 (pm20) REVERT: B 487 GLU cc_start: 0.8325 (pt0) cc_final: 0.7924 (pt0) REVERT: B 586 ARG cc_start: 0.9410 (mmm-85) cc_final: 0.9200 (mmm-85) REVERT: C 463 MET cc_start: 0.5207 (mpp) cc_final: 0.4663 (mpp) REVERT: C 485 ARG cc_start: -0.1703 (mtt180) cc_final: -0.3111 (mtt90) REVERT: C 496 MET cc_start: 0.0557 (ptm) cc_final: -0.0609 (tmm) REVERT: C 586 ARG cc_start: 0.9199 (mtp85) cc_final: 0.8950 (ttm110) REVERT: C 813 GLU cc_start: 0.9055 (tt0) cc_final: 0.8675 (tp30) REVERT: D 503 MET cc_start: 0.7056 (tmm) cc_final: 0.6575 (tmm) REVERT: D 519 ASP cc_start: 0.9003 (m-30) cc_final: 0.8534 (t70) REVERT: D 668 ASP cc_start: 0.8193 (m-30) cc_final: 0.7875 (m-30) REVERT: E 147 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9228 (mt) REVERT: E 191 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8948 (mm-30) REVERT: F 24 MET cc_start: 0.9218 (tpt) cc_final: 0.8694 (tpt) REVERT: F 57 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7304 (m) REVERT: F 174 TYR cc_start: 0.8435 (p90) cc_final: 0.8206 (p90) REVERT: F 176 TYR cc_start: 0.9015 (m-80) cc_final: 0.8526 (m-80) REVERT: F 207 GLN cc_start: 0.9138 (pt0) cc_final: 0.8739 (pp30) REVERT: G 10 MET cc_start: 0.8433 (ptt) cc_final: 0.8180 (ptt) REVERT: G 24 MET cc_start: 0.8852 (tpt) cc_final: 0.8493 (tpp) REVERT: G 41 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6640 (ptpp) REVERT: G 76 LEU cc_start: 0.8866 (mm) cc_final: 0.8500 (tp) REVERT: G 185 LEU cc_start: 0.9424 (tt) cc_final: 0.9164 (tt) REVERT: H 6 ARG cc_start: 0.8102 (tmt170) cc_final: 0.7747 (ttp80) REVERT: H 10 MET cc_start: 0.8418 (tmm) cc_final: 0.7933 (tmm) REVERT: H 13 THR cc_start: 0.9078 (m) cc_final: 0.8855 (t) REVERT: H 58 MET cc_start: 0.8283 (tpp) cc_final: 0.8024 (tpp) REVERT: H 95 GLU cc_start: 0.9080 (tt0) cc_final: 0.8420 (tm-30) outliers start: 51 outliers final: 28 residues processed: 297 average time/residue: 0.1158 time to fit residues: 52.0046 Evaluate side-chains 267 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 420 ARG 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 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 28 VAL Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 147 LEU 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 192 MET Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 153 ILE 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 109 ILE Chi-restraints excluded: chain H residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 122 optimal weight: 0.0980 chunk 216 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.152453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100176 restraints weight = 74091.602| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 7.93 r_work: 0.3035 rms_B_bonded: 6.24 restraints_weight: 2.0000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17370 Z= 0.191 Angle : 0.616 8.101 23595 Z= 0.324 Chirality : 0.042 0.180 2733 Planarity : 0.004 0.041 2896 Dihedral : 3.813 21.555 2425 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.15 % Allowed : 19.42 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2218 helix: 2.53 (0.14), residues: 1325 sheet: -1.23 (0.43), residues: 137 loop : -1.24 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 37 TYR 0.015 0.001 TYR D 647 PHE 0.027 0.002 PHE D 607 TRP 0.027 0.002 TRP C 671 HIS 0.052 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00444 (17358) covalent geometry : angle 0.61533 (23571) SS BOND : bond 0.00595 ( 12) SS BOND : angle 1.30685 ( 24) hydrogen bonds : bond 0.04054 ( 1098) hydrogen bonds : angle 4.04672 ( 3258) *********************** 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 314 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.644 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: 0.7407 (ptm) cc_final: 0.6132 (ppp) REVERT: A 503 MET cc_start: 0.6224 (tmm) cc_final: 0.5292 (tmm) REVERT: A 720 THR cc_start: 0.6705 (OUTLIER) cc_final: 0.6455 (p) REVERT: B 407 MET cc_start: 0.6413 (mmm) cc_final: 0.6162 (mmm) REVERT: B 408 MET cc_start: 0.2483 (mpp) cc_final: 0.2262 (mmm) REVERT: B 586 ARG cc_start: 0.9497 (mmm-85) cc_final: 0.9288 (mmm-85) REVERT: B 688 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: C 485 ARG cc_start: -0.1971 (mtt180) cc_final: -0.3210 (mtt90) REVERT: C 496 MET cc_start: 0.1710 (ptm) cc_final: 0.0433 (tmm) REVERT: C 524 GLU cc_start: 0.8973 (mp0) cc_final: 0.8760 (mp0) REVERT: C 669 LYS cc_start: 0.5782 (tptt) cc_final: 0.5284 (tppt) REVERT: C 813 GLU cc_start: 0.9191 (tt0) cc_final: 0.8882 (tp30) REVERT: D 503 MET cc_start: 0.7038 (tmm) cc_final: 0.6819 (tmm) REVERT: D 519 ASP cc_start: 0.9287 (m-30) cc_final: 0.8803 (t70) REVERT: D 524 GLU cc_start: 0.9036 (mp0) cc_final: 0.8756 (mp0) REVERT: D 668 ASP cc_start: 0.8388 (m-30) cc_final: 0.8110 (m-30) REVERT: E 117 MET cc_start: 0.9147 (mmm) cc_final: 0.8930 (mmm) REVERT: E 147 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9318 (mt) REVERT: F 24 MET cc_start: 0.9401 (tpt) cc_final: 0.9012 (tpt) REVERT: F 63 LEU cc_start: 0.9338 (tp) cc_final: 0.9133 (tp) REVERT: F 69 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7048 (pp) REVERT: F 70 GLU cc_start: 0.7769 (mp0) cc_final: 0.7108 (pp20) REVERT: F 128 TYR cc_start: 0.8210 (t80) cc_final: 0.7629 (t80) REVERT: G 10 MET cc_start: 0.8346 (ptt) cc_final: 0.7942 (ptt) REVERT: G 24 MET cc_start: 0.9022 (tpt) cc_final: 0.8109 (tpt) REVERT: G 41 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6448 (ptpp) REVERT: G 76 LEU cc_start: 0.8960 (mm) cc_final: 0.8556 (tp) REVERT: G 185 LEU cc_start: 0.9425 (tt) cc_final: 0.9201 (tp) REVERT: H 6 ARG cc_start: 0.8364 (tmt170) cc_final: 0.8019 (ttp80) REVERT: H 10 MET cc_start: 0.8416 (tmm) cc_final: 0.8214 (tmm) REVERT: H 109 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9117 (pt) outliers start: 69 outliers final: 42 residues processed: 292 average time/residue: 0.1387 time to fit residues: 60.4892 Evaluate side-chains 267 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 591 ILE Chi-restraints excluded: chain A residue 601 VAL 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 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain B residue 789 LEU 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 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 703 LEU 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 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 147 LEU 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 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 153 ILE 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 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 112 VAL Chi-restraints excluded: chain H residue 150 ILE 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 222 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 186 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4415 r_free = 0.4415 target = 0.153937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098253 restraints weight = 94765.557| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 8.07 r_work: 0.3083 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6364 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= 0.124 Angle : 0.573 9.170 23595 Z= 0.296 Chirality : 0.041 0.178 2733 Planarity : 0.003 0.043 2896 Dihedral : 3.760 18.566 2425 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.65 % Allowed : 21.23 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.19), residues: 2218 helix: 2.68 (0.14), residues: 1324 sheet: -1.05 (0.44), residues: 136 loop : -1.14 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 586 TYR 0.009 0.001 TYR C 732 PHE 0.018 0.001 PHE F 73 TRP 0.014 0.001 TRP C 671 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00283 (17358) covalent geometry : angle 0.57142 (23571) SS BOND : bond 0.00412 ( 12) SS BOND : angle 1.36528 ( 24) hydrogen bonds : bond 0.03629 ( 1098) hydrogen bonds : angle 3.86569 ( 3258) *********************** 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 290 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.570 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: A 496 MET cc_start: 0.7541 (ptm) cc_final: 0.6240 (ppp) REVERT: B 408 MET cc_start: 0.2404 (mpp) cc_final: 0.1791 (mmm) REVERT: B 422 GLU cc_start: 0.8496 (tp30) cc_final: 0.7769 (mp0) REVERT: B 619 ASN cc_start: 0.9466 (t0) cc_final: 0.9177 (m-40) REVERT: B 688 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6973 (pt0) REVERT: C 463 MET cc_start: 0.5185 (mpp) cc_final: 0.4706 (mpp) REVERT: C 485 ARG cc_start: -0.2019 (mtt180) cc_final: -0.3323 (mtt90) REVERT: C 496 MET cc_start: 0.1552 (ptm) cc_final: 0.0490 (tmm) REVERT: C 669 LYS cc_start: 0.5921 (tptt) cc_final: 0.5378 (tppt) REVERT: C 813 GLU cc_start: 0.9168 (tt0) cc_final: 0.8843 (tp30) REVERT: D 473 ASP cc_start: 0.8194 (m-30) cc_final: 0.7668 (p0) REVERT: D 503 MET cc_start: 0.7082 (tmm) cc_final: 0.6866 (tmm) REVERT: D 519 ASP cc_start: 0.9203 (m-30) cc_final: 0.8731 (t70) REVERT: D 524 GLU cc_start: 0.9063 (mp0) cc_final: 0.8844 (mp0) REVERT: D 668 ASP cc_start: 0.8404 (m-30) cc_final: 0.8157 (m-30) REVERT: D 692 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8050 (ptm160) REVERT: E 205 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: F 70 GLU cc_start: 0.7832 (mp0) cc_final: 0.7146 (pp20) REVERT: F 128 TYR cc_start: 0.8263 (t80) cc_final: 0.7790 (t80) REVERT: G 6 ARG cc_start: 0.7450 (tpt90) cc_final: 0.7090 (tpt90) REVERT: G 10 MET cc_start: 0.8271 (ptt) cc_final: 0.7993 (ptt) REVERT: G 24 MET cc_start: 0.9009 (tpt) cc_final: 0.8108 (tpt) REVERT: G 41 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6700 (ptpp) REVERT: G 76 LEU cc_start: 0.8932 (mm) cc_final: 0.8544 (tp) REVERT: G 185 LEU cc_start: 0.9411 (tt) cc_final: 0.9175 (tp) REVERT: H 6 ARG cc_start: 0.8407 (tmt170) cc_final: 0.8061 (ttp80) REVERT: H 109 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8968 (pt) outliers start: 44 outliers final: 24 residues processed: 273 average time/residue: 0.1272 time to fit residues: 51.7533 Evaluate side-chains 255 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 464 VAL 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 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS 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 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 109 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS C 587 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.153400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096629 restraints weight = 77603.075| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 6.14 r_work: 0.3120 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17370 Z= 0.123 Angle : 0.581 9.969 23595 Z= 0.297 Chirality : 0.040 0.217 2733 Planarity : 0.003 0.044 2896 Dihedral : 3.666 18.370 2425 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.01 % Allowed : 20.87 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.19), residues: 2218 helix: 2.72 (0.14), residues: 1329 sheet: -1.08 (0.45), residues: 136 loop : -1.01 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 204 TYR 0.013 0.001 TYR E 128 PHE 0.017 0.001 PHE F 73 TRP 0.013 0.001 TRP C 671 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00279 (17358) covalent geometry : angle 0.57803 (23571) SS BOND : bond 0.00600 ( 12) SS BOND : angle 1.78885 ( 24) hydrogen bonds : bond 0.03463 ( 1098) hydrogen bonds : angle 3.80924 ( 3258) *********************** 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 297 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.658 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 463 MET cc_start: 0.6352 (mpp) cc_final: 0.5380 (mmt) REVERT: A 496 MET cc_start: 0.7381 (ptm) cc_final: 0.6916 (ppp) REVERT: A 655 THR cc_start: 0.3075 (OUTLIER) cc_final: 0.2850 (t) REVERT: B 408 MET cc_start: 0.1537 (mpp) cc_final: 0.0967 (mmm) REVERT: B 422 GLU cc_start: 0.8486 (tp30) cc_final: 0.7724 (pm20) REVERT: B 688 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6835 (pt0) REVERT: C 463 MET cc_start: 0.5239 (mpp) cc_final: 0.4717 (mpp) REVERT: C 485 ARG cc_start: -0.1959 (mtt180) cc_final: -0.3338 (mtt90) REVERT: C 496 MET cc_start: 0.1147 (ptm) cc_final: 0.0013 (tmm) REVERT: C 669 LYS cc_start: 0.5609 (tptt) cc_final: 0.5075 (tppt) REVERT: C 813 GLU cc_start: 0.9085 (tt0) cc_final: 0.8849 (tp30) REVERT: D 473 ASP cc_start: 0.7994 (m-30) cc_final: 0.7466 (p0) REVERT: D 496 MET cc_start: 0.7119 (tpp) cc_final: 0.6555 (tpp) REVERT: D 519 ASP cc_start: 0.9184 (m-30) cc_final: 0.8707 (t70) REVERT: D 668 ASP cc_start: 0.8478 (m-30) cc_final: 0.8209 (m-30) REVERT: E 101 VAL cc_start: 0.9310 (t) cc_final: 0.8960 (p) REVERT: E 191 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8874 (mm-30) REVERT: E 203 ASP cc_start: 0.9451 (t0) cc_final: 0.9152 (t70) REVERT: F 24 MET cc_start: 0.9416 (tpt) cc_final: 0.9201 (tpt) REVERT: F 37 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6273 (ptt-90) REVERT: F 70 GLU cc_start: 0.7777 (mp0) cc_final: 0.7376 (pp20) REVERT: F 120 LEU cc_start: 0.9160 (mt) cc_final: 0.8888 (tt) REVERT: F 128 TYR cc_start: 0.8176 (t80) cc_final: 0.7669 (t80) REVERT: G 6 ARG cc_start: 0.7262 (tpt90) cc_final: 0.6885 (tpt90) REVERT: G 41 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5407 (ptpp) REVERT: G 76 LEU cc_start: 0.8973 (mm) cc_final: 0.8722 (tp) REVERT: G 185 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9111 (tp) REVERT: H 6 ARG cc_start: 0.8408 (tmt170) cc_final: 0.7863 (ttp80) REVERT: H 109 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9014 (pt) outliers start: 50 outliers final: 35 residues processed: 279 average time/residue: 0.1415 time to fit residues: 58.4192 Evaluate side-chains 272 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 464 VAL 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 D residue 709 ASN Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 10 MET 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 205 HIS 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 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 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 172 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4412 r_free = 0.4412 target = 0.152881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098123 restraints weight = 96187.439| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 8.07 r_work: 0.3061 rms_B_bonded: 6.61 restraints_weight: 2.0000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17370 Z= 0.122 Angle : 0.581 11.362 23595 Z= 0.297 Chirality : 0.040 0.260 2733 Planarity : 0.003 0.048 2896 Dihedral : 3.657 19.522 2425 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.71 % Allowed : 21.53 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.19), residues: 2218 helix: 2.75 (0.14), residues: 1329 sheet: -0.94 (0.46), residues: 132 loop : -0.94 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 204 TYR 0.010 0.001 TYR E 128 PHE 0.016 0.001 PHE F 73 TRP 0.010 0.001 TRP A 460 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00278 (17358) covalent geometry : angle 0.57778 (23571) SS BOND : bond 0.00742 ( 12) SS BOND : angle 1.87809 ( 24) hydrogen bonds : bond 0.03404 ( 1098) hydrogen bonds : angle 3.78358 ( 3258) *********************** 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 287 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.686 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 408 MET cc_start: 0.6498 (mmm) cc_final: 0.6176 (mmm) REVERT: A 463 MET cc_start: 0.6541 (mpp) cc_final: 0.5138 (mmt) REVERT: A 496 MET cc_start: 0.7567 (ptm) cc_final: 0.6979 (ppp) REVERT: A 655 THR cc_start: 0.3242 (OUTLIER) cc_final: 0.3013 (t) REVERT: B 674 MET cc_start: 0.1905 (ptp) cc_final: 0.1162 (ptm) REVERT: B 688 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6862 (pt0) REVERT: C 463 MET cc_start: 0.5321 (mpp) cc_final: 0.5063 (mpp) REVERT: C 485 ARG cc_start: -0.1921 (mtt180) cc_final: -0.3307 (mtt90) REVERT: C 496 MET cc_start: 0.1336 (ptm) cc_final: 0.0320 (tmm) REVERT: C 586 ARG cc_start: 0.9284 (mmm-85) cc_final: 0.8870 (ttm110) REVERT: C 669 LYS cc_start: 0.5979 (tptt) cc_final: 0.5533 (tppt) REVERT: C 813 GLU cc_start: 0.9169 (tt0) cc_final: 0.8907 (tp30) REVERT: D 473 ASP cc_start: 0.8049 (m-30) cc_final: 0.7502 (p0) REVERT: D 496 MET cc_start: 0.7315 (tpp) cc_final: 0.6836 (tpp) REVERT: D 503 MET cc_start: 0.7591 (tmm) cc_final: 0.6835 (tmm) REVERT: D 519 ASP cc_start: 0.9260 (m-30) cc_final: 0.8771 (t70) REVERT: D 669 LYS cc_start: 0.8401 (pttp) cc_final: 0.8051 (pptt) REVERT: E 140 ILE cc_start: 0.9398 (mm) cc_final: 0.9119 (pt) REVERT: E 203 ASP cc_start: 0.9499 (t0) cc_final: 0.9219 (t70) REVERT: F 37 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6306 (ptt-90) REVERT: F 70 GLU cc_start: 0.7940 (mp0) cc_final: 0.7467 (pp20) REVERT: F 120 LEU cc_start: 0.9113 (mt) cc_final: 0.8851 (tt) REVERT: F 128 TYR cc_start: 0.8159 (t80) cc_final: 0.7703 (t80) REVERT: G 6 ARG cc_start: 0.7269 (tpt90) cc_final: 0.6737 (tpt90) REVERT: G 41 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6693 (pttm) REVERT: G 117 MET cc_start: 0.9069 (mmp) cc_final: 0.8641 (mtt) REVERT: G 160 ASN cc_start: 0.8494 (m-40) cc_final: 0.8267 (m-40) REVERT: G 185 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9066 (tt) REVERT: H 6 ARG cc_start: 0.8577 (tmt170) cc_final: 0.8211 (ttp80) REVERT: H 80 ILE cc_start: 0.8846 (mp) cc_final: 0.8606 (mp) REVERT: H 109 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9048 (pt) outliers start: 45 outliers final: 32 residues processed: 268 average time/residue: 0.1484 time to fit residues: 58.9927 Evaluate side-chains 261 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 THR 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 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain C residue 407 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 547 SER 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 D residue 720 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS 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 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 199 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 141 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 461 ASN ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.145739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090224 restraints weight = 88343.725| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 7.62 r_work: 0.2929 rms_B_bonded: 6.38 restraints_weight: 2.0000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 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 = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17370 Z= 0.271 Angle : 0.717 12.581 23595 Z= 0.373 Chirality : 0.045 0.246 2733 Planarity : 0.004 0.056 2896 Dihedral : 4.142 21.561 2425 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.19 % Allowed : 21.77 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.18), residues: 2218 helix: 2.31 (0.14), residues: 1324 sheet: -1.02 (0.50), residues: 125 loop : -1.01 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 204 TYR 0.016 0.002 TYR H 156 PHE 0.018 0.002 PHE C 659 TRP 0.019 0.002 TRP C 766 HIS 0.008 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00627 (17358) covalent geometry : angle 0.71464 (23571) SS BOND : bond 0.00700 ( 12) SS BOND : angle 2.02912 ( 24) hydrogen bonds : bond 0.04589 ( 1098) hydrogen bonds : angle 4.30214 ( 3258) *********************** 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 269 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.666 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: 0.7911 (ptm) cc_final: 0.7222 (ppp) REVERT: B 408 MET cc_start: 0.3238 (mmt) cc_final: 0.2878 (mmm) REVERT: B 688 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: C 485 ARG cc_start: -0.1478 (mtt180) cc_final: -0.3104 (mtt90) REVERT: C 519 ASP cc_start: 0.9473 (m-30) cc_final: 0.9264 (m-30) REVERT: C 647 TYR cc_start: 0.3822 (p90) cc_final: 0.2443 (p90) REVERT: C 669 LYS cc_start: 0.6187 (tptt) cc_final: 0.5707 (tppt) REVERT: C 813 GLU cc_start: 0.9234 (tt0) cc_final: 0.8983 (mm-30) REVERT: D 473 ASP cc_start: 0.8166 (m-30) cc_final: 0.7542 (p0) REVERT: D 519 ASP cc_start: 0.9359 (m-30) cc_final: 0.8940 (t70) REVERT: E 203 ASP cc_start: 0.9482 (t0) cc_final: 0.9236 (t70) REVERT: E 205 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8314 (t-90) REVERT: F 70 GLU cc_start: 0.8067 (mp0) cc_final: 0.7786 (pp20) REVERT: F 128 TYR cc_start: 0.8281 (t80) cc_final: 0.7359 (t80) REVERT: G 117 MET cc_start: 0.9178 (mmp) cc_final: 0.8678 (mtt) REVERT: G 185 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9229 (tp) REVERT: H 109 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9227 (pt) REVERT: H 199 HIS cc_start: 0.9422 (OUTLIER) cc_final: 0.9033 (t-170) outliers start: 53 outliers final: 37 residues processed: 254 average time/residue: 0.1579 time to fit residues: 58.0992 Evaluate side-chains 242 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 633 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 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain C residue 407 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 547 SER 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 11 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 24 MET 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 205 HIS 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 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 134 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 16 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 63 optimal weight: 0.0270 chunk 64 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 209 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 161 optimal weight: 0.0270 overall best weight: 1.1300 ------------------------------------------------------------------------------- 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 ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.148295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093458 restraints weight = 90560.533| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 7.78 r_work: 0.2993 rms_B_bonded: 6.43 restraints_weight: 2.0000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17370 Z= 0.139 Angle : 0.638 12.215 23595 Z= 0.324 Chirality : 0.041 0.204 2733 Planarity : 0.003 0.045 2896 Dihedral : 3.928 19.954 2425 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.47 % Allowed : 23.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.19), residues: 2218 helix: 2.58 (0.14), residues: 1326 sheet: -0.78 (0.49), residues: 134 loop : -0.97 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 694 TYR 0.011 0.001 TYR A 732 PHE 0.016 0.001 PHE F 73 TRP 0.018 0.001 TRP A 460 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00320 (17358) covalent geometry : angle 0.63640 (23571) SS BOND : bond 0.00602 ( 12) SS BOND : angle 1.61794 ( 24) hydrogen bonds : bond 0.03809 ( 1098) hydrogen bonds : angle 3.92473 ( 3258) ********************** 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 263 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7888 (ptm) cc_final: 0.7368 (ppp) REVERT: B 408 MET cc_start: 0.3269 (mmt) cc_final: 0.3005 (mmm) REVERT: B 668 ASP cc_start: 0.7820 (t0) cc_final: 0.7584 (m-30) REVERT: B 688 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: C 463 MET cc_start: 0.5351 (mpp) cc_final: 0.5129 (mpp) REVERT: C 485 ARG cc_start: -0.1500 (mtt180) cc_final: -0.2969 (mtt90) REVERT: C 496 MET cc_start: 0.0337 (ptm) cc_final: -0.0254 (tmm) REVERT: C 519 ASP cc_start: 0.9464 (m-30) cc_final: 0.9250 (m-30) REVERT: C 647 TYR cc_start: 0.4657 (p90) cc_final: 0.2841 (p90) REVERT: C 669 LYS cc_start: 0.6171 (tptt) cc_final: 0.5735 (tppt) REVERT: C 813 GLU cc_start: 0.9214 (tt0) cc_final: 0.8957 (mm-30) REVERT: D 473 ASP cc_start: 0.8147 (m-30) cc_final: 0.7531 (p0) REVERT: D 503 MET cc_start: 0.7738 (tmm) cc_final: 0.7313 (tmm) REVERT: D 519 ASP cc_start: 0.9314 (m-30) cc_final: 0.8844 (t70) REVERT: D 669 LYS cc_start: 0.8577 (pttp) cc_final: 0.8279 (pptt) REVERT: D 692 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8195 (ptm160) REVERT: D 721 MET cc_start: 0.7373 (ppp) cc_final: 0.7005 (mmt) REVERT: E 205 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: F 70 GLU cc_start: 0.8162 (mp0) cc_final: 0.7847 (pp20) REVERT: F 128 TYR cc_start: 0.8355 (t80) cc_final: 0.7628 (t80) REVERT: G 185 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9134 (tt) REVERT: H 97 PHE cc_start: 0.8981 (t80) cc_final: 0.8630 (t80) REVERT: H 109 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9058 (pt) REVERT: H 192 MET cc_start: 0.9146 (mtm) cc_final: 0.8674 (mmt) outliers start: 41 outliers final: 33 residues processed: 250 average time/residue: 0.1464 time to fit residues: 54.0763 Evaluate side-chains 248 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 ILE 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 B residue 688 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 547 SER 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 148 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 59 THR 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 205 HIS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.147102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090481 restraints weight = 64882.120| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 6.30 r_work: 0.3023 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17370 Z= 0.182 Angle : 0.660 11.955 23595 Z= 0.337 Chirality : 0.041 0.200 2733 Planarity : 0.004 0.045 2896 Dihedral : 3.915 19.950 2425 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.53 % Allowed : 23.51 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 2218 helix: 2.56 (0.14), residues: 1325 sheet: -0.91 (0.50), residues: 130 loop : -0.92 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 694 TYR 0.020 0.001 TYR A 440 PHE 0.017 0.001 PHE F 73 TRP 0.023 0.001 TRP A 460 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00423 (17358) covalent geometry : angle 0.65877 (23571) SS BOND : bond 0.00610 ( 12) SS BOND : angle 1.54261 ( 24) hydrogen bonds : bond 0.03902 ( 1098) hydrogen bonds : angle 4.00221 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5542.50 seconds wall clock time: 95 minutes 11.92 seconds (5711.92 seconds total)