Starting phenix.real_space_refine on Mon Jun 16 12:07:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3s_17393/06_2025/8p3s_17393.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 127 5.16 5 C 11954 2.51 5 N 2866 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18195 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 3125 Chain: "B" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3077 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3015 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 3122 Chain: "E" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 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: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1359 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 14.69, per 1000 atoms: 0.81 Number of scatterers: 18195 At special positions: 0 Unit cell: (118.531, 127.204, 137.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 P 5 15.00 O 3243 8.00 N 2866 7.00 C 11954 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=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 3.5 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 26 sheets defined 60.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.727A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.678A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.531A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.599A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.665A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 629 removed outlier: 3.735A pdb=" N ARG B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.675A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.542A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.590A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.113A 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 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.686A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for '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 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.732A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.539A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.765A 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 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.743A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.619A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.678A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.545A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.539A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 161 removed outlier: 3.728A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.506A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.900A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.740A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.091A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 162 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.944A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 Processing helix chain 'H' and resid 177 through 210 removed outlier: 4.030A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 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 496 through 498 removed outlier: 3.847A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.338A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 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 496 through 498 removed outlier: 3.823A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.316A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 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 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.847A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.352A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 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 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.833A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.327A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.794A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 65 through 67 1131 hydrogen bonds defined for protein. 3272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2816 1.31 - 1.44: 5174 1.44 - 1.57: 10374 1.57 - 1.71: 10 1.71 - 1.84: 206 Bond restraints: 18580 Sorted by residual: bond pdb=" C PRO B 512 " pdb=" O PRO B 512 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.13e-02 7.83e+03 2.34e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.94e+01 bond pdb=" N VAL C 488 " pdb=" CA VAL C 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C LYS A 506 " pdb=" O LYS A 506 " ideal model delta sigma weight residual 1.238 1.183 0.055 1.28e-02 6.10e+03 1.84e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 ... (remaining 18575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22193 2.24 - 4.48: 2617 4.48 - 6.71: 193 6.71 - 8.95: 27 8.95 - 11.19: 8 Bond angle restraints: 25038 Sorted by residual: angle pdb=" O LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 121.32 110.49 10.83 1.15e+00 7.56e-01 8.88e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.62 9.26 1.23e+00 6.61e-01 5.67e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.80 100.86 9.94 1.51e+00 4.39e-01 4.33e+01 angle pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.84 111.94 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N PRO B 632 " pdb=" CA PRO B 632 " pdb=" CB PRO B 632 " ideal model delta sigma weight residual 103.25 96.64 6.61 1.05e+00 9.07e-01 3.97e+01 ... (remaining 25033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 10376 29.03 - 58.07: 435 58.07 - 87.10: 52 87.10 - 116.14: 8 116.14 - 145.17: 2 Dihedral angle restraints: 10873 sinusoidal: 4263 harmonic: 6610 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 23.57 69.43 1 1.00e+01 1.00e-02 6.23e+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 35.60 57.40 1 1.00e+01 1.00e-02 4.43e+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 43.29 49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 10870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2587 0.173 - 0.347: 197 0.347 - 0.520: 8 0.520 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB VAL A 626 " pdb=" CA VAL A 626 " pdb=" CG1 VAL A 626 " pdb=" CG2 VAL A 626 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CG LEU D 483 " pdb=" CB LEU D 483 " pdb=" CD1 LEU D 483 " pdb=" CD2 LEU D 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2790 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 628 " 0.693 9.50e-02 1.11e+02 3.11e-01 5.88e+01 pdb=" NE ARG B 628 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 628 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 628 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 628 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " 0.033 2.00e-02 2.50e+03 6.76e-02 4.56e+01 pdb=" C BPHE D 574 " -0.117 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " 0.044 2.00e-02 2.50e+03 pdb=" N ASN D 575 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 675 " -0.601 9.50e-02 1.11e+02 2.70e-01 4.44e+01 pdb=" NE ARG D 675 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 675 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 675 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 675 " -0.021 2.00e-02 2.50e+03 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2409 2.75 - 3.29: 18613 3.29 - 3.83: 29986 3.83 - 4.36: 37700 4.36 - 4.90: 62814 Nonbonded interactions: 151522 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.216 3.040 nonbonded pdb=" O GLU B 627 " pdb=" N MET B 629 " model vdw 2.254 3.120 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.271 3.120 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.287 3.040 ... (remaining 151517 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 506 or resid 510 through 573 or resid 575 thro \ ugh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) o \ r resid 595 through 622 or resid 624 through 626 or (resid 633 through 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 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 823 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'B' and (resid 393 through 506 or resid 510 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 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 622 or resid 624 through 626 or (res \ id 633 through 634 and (name N or name CA or name C or name O or name CB )) or r \ esid 635 through 773 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 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 through 622 or resid 624 \ through 626 or (resid 633 through 634 and (name N or name CA or name C or name O \ or name CB )) or resid 635 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 'D' and (resid 393 through 506 or resid 510 through 551 or (resid 569 and \ (name N or name CA or name C or name O or name CB )) or resid 570 through 573 o \ r resid 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C or na \ me O or name CB )) or resid 595 through 622 or resid 624 through 626 or resid 63 \ 3 through 773 or (resid 784 and (name N or name CA or name C or name O or name C \ B )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 20 \ 3 or (resid 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 through 206 or (resid 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or ( \ resid 206 through 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 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: 1.330 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: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.300 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 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 : 0.012 0.064 18592 Z= 0.893 Angle : 1.461 11.189 25062 Z= 1.037 Chirality : 0.107 0.866 2793 Planarity : 0.015 0.311 3050 Dihedral : 15.799 145.169 6629 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.26 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 3.66 % Favored : 94.54 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2268 helix: 0.97 (0.14), residues: 1332 sheet: -1.68 (0.37), residues: 107 loop : -1.98 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP B 578 HIS 0.011 0.003 HIS E 60 PHE 0.021 0.005 PHE A 517 TYR 0.034 0.005 TYR B 469 ARG 0.016 0.002 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.13525 ( 1131) hydrogen bonds : angle 5.28407 ( 3272) SS BOND : bond 0.01439 ( 12) SS BOND : angle 3.08345 ( 24) covalent geometry : bond 0.01250 (18580) covalent geometry : angle 1.45848 (25038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 2.176 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: A 591 ILE cc_start: 0.8820 (tp) cc_final: 0.8549 (pt) REVERT: B 585 MET cc_start: 0.8907 (mmt) cc_final: 0.8300 (mmt) REVERT: E 81 ASP cc_start: 0.8323 (t0) cc_final: 0.7968 (p0) REVERT: E 92 ASP cc_start: 0.7509 (t0) cc_final: 0.7065 (p0) REVERT: E 207 GLN cc_start: 0.8904 (mm110) cc_final: 0.8653 (tm-30) REVERT: F 24 MET cc_start: 0.9162 (tpt) cc_final: 0.8905 (tpt) REVERT: F 61 SER cc_start: 0.9389 (t) cc_final: 0.9060 (p) REVERT: F 65 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7997 (mtm110) REVERT: F 81 ASP cc_start: 0.8811 (t0) cc_final: 0.8584 (t70) REVERT: F 98 LEU cc_start: 0.8486 (tt) cc_final: 0.8235 (mm) REVERT: F 126 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9191 (tm-30) REVERT: G 13 THR cc_start: 0.9374 (t) cc_final: 0.9027 (p) REVERT: G 81 ASP cc_start: 0.9230 (p0) cc_final: 0.8832 (t0) REVERT: G 84 PRO cc_start: 0.5605 (Cg_exo) cc_final: 0.5203 (Cg_endo) REVERT: G 99 ARG cc_start: 0.9299 (mtt-85) cc_final: 0.8961 (mtm180) REVERT: H 6 ARG cc_start: 0.8404 (tmt-80) cc_final: 0.8176 (tmm160) REVERT: H 10 MET cc_start: 0.9034 (tpp) cc_final: 0.8704 (tpp) REVERT: H 13 THR cc_start: 0.9102 (m) cc_final: 0.8697 (t) REVERT: H 35 TYR cc_start: 0.8828 (m-80) cc_final: 0.8553 (m-80) REVERT: H 61 SER cc_start: 0.9502 (t) cc_final: 0.8932 (p) REVERT: H 70 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8495 (pp20) REVERT: H 74 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8999 (ttmm) outliers start: 33 outliers final: 8 residues processed: 392 average time/residue: 1.4390 time to fit residues: 625.8411 Evaluate side-chains 203 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.154606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087575 restraints weight = 86483.779| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 5.44 r_work: 0.2955 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 18592 Z= 0.145 Angle : 0.664 17.640 25062 Z= 0.345 Chirality : 0.043 0.230 2793 Planarity : 0.004 0.040 3050 Dihedral : 11.468 104.561 2841 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 2.24 % Allowed : 13.44 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2268 helix: 2.21 (0.14), residues: 1341 sheet: -1.46 (0.36), residues: 154 loop : -1.38 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.032 0.002 PHE A 658 TYR 0.016 0.001 TYR D 711 ARG 0.009 0.001 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 1131) hydrogen bonds : angle 4.13926 ( 3272) SS BOND : bond 0.00555 ( 12) SS BOND : angle 2.40465 ( 24) covalent geometry : bond 0.00324 (18580) covalent geometry : angle 0.65974 (25038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 1.919 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 762 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.6018 (tp) REVERT: B 496 MET cc_start: 0.7189 (mtp) cc_final: 0.6954 (mtt) REVERT: B 506 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8610 (ptpp) REVERT: B 708 MET cc_start: 0.8954 (mpp) cc_final: 0.8705 (mpp) REVERT: C 407 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6148 (mpp) REVERT: C 414 MET cc_start: 0.1669 (mtm) cc_final: 0.1337 (mtp) REVERT: C 460 TRP cc_start: 0.4550 (OUTLIER) cc_final: 0.4233 (t-100) REVERT: C 496 MET cc_start: 0.0685 (mtp) cc_final: 0.0397 (mtp) REVERT: C 674 MET cc_start: -0.4987 (ptm) cc_final: -0.5210 (ptp) REVERT: D 407 MET cc_start: 0.7639 (mpp) cc_final: 0.7382 (mpp) REVERT: D 414 MET cc_start: 0.5991 (mpt) cc_final: 0.5302 (tmt) REVERT: D 503 MET cc_start: 0.5201 (tpt) cc_final: 0.4685 (tpt) REVERT: E 95 GLU cc_start: 0.8668 (mp0) cc_final: 0.8403 (mp0) REVERT: F 24 MET cc_start: 0.9200 (tpt) cc_final: 0.8937 (tpt) REVERT: F 61 SER cc_start: 0.9154 (t) cc_final: 0.8686 (p) REVERT: F 65 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7703 (mtm110) REVERT: F 67 CYS cc_start: 0.7405 (m) cc_final: 0.7020 (m) REVERT: F 81 ASP cc_start: 0.8491 (t0) cc_final: 0.8120 (t70) REVERT: F 126 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9021 (tm-30) REVERT: G 13 THR cc_start: 0.9128 (t) cc_final: 0.8853 (p) REVERT: G 58 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: G 81 ASP cc_start: 0.8934 (p0) cc_final: 0.8547 (t0) REVERT: G 176 TYR cc_start: 0.9505 (m-80) cc_final: 0.9294 (m-80) REVERT: G 203 ASP cc_start: 0.8447 (m-30) cc_final: 0.7724 (m-30) REVERT: H 10 MET cc_start: 0.8701 (tpp) cc_final: 0.8500 (tpp) REVERT: H 34 LEU cc_start: 0.9002 (tp) cc_final: 0.8584 (tp) REVERT: H 35 TYR cc_start: 0.8720 (m-80) cc_final: 0.8490 (m-80) REVERT: H 61 SER cc_start: 0.9117 (t) cc_final: 0.8021 (p) REVERT: H 70 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8454 (pp20) REVERT: H 81 ASP cc_start: 0.9197 (t0) cc_final: 0.8904 (t0) REVERT: H 115 LEU cc_start: 0.9296 (mt) cc_final: 0.8985 (mt) outliers start: 41 outliers final: 7 residues processed: 262 average time/residue: 1.4275 time to fit residues: 415.2943 Evaluate side-chains 191 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 58 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 219 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 205 HIS F 60 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079297 restraints weight = 71033.611| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.15 r_work: 0.2942 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18592 Z= 0.199 Angle : 0.640 15.831 25062 Z= 0.334 Chirality : 0.043 0.234 2793 Planarity : 0.004 0.043 3050 Dihedral : 10.659 85.143 2828 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.16 % Rotamer: Outliers : 3.17 % Allowed : 14.53 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2268 helix: 2.31 (0.14), residues: 1348 sheet: -1.05 (0.38), residues: 155 loop : -1.10 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 460 HIS 0.004 0.001 HIS E 60 PHE 0.022 0.002 PHE A 658 TYR 0.028 0.002 TYR A 405 ARG 0.010 0.001 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1131) hydrogen bonds : angle 4.14702 ( 3272) SS BOND : bond 0.00661 ( 12) SS BOND : angle 2.04507 ( 24) covalent geometry : bond 0.00464 (18580) covalent geometry : angle 0.63742 (25038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.917 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 408 MET cc_start: 0.7754 (mpt) cc_final: 0.6070 (mmt) REVERT: A 463 MET cc_start: 0.5593 (mtm) cc_final: 0.5133 (mmm) REVERT: A 496 MET cc_start: 0.7086 (tmm) cc_final: 0.6738 (tmm) REVERT: B 659 PHE cc_start: 0.8108 (t80) cc_final: 0.7214 (t80) REVERT: B 714 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8602 (pm20) REVERT: C 414 MET cc_start: 0.1875 (mtm) cc_final: 0.1601 (mtp) REVERT: C 460 TRP cc_start: 0.4411 (OUTLIER) cc_final: 0.3615 (t-100) REVERT: C 674 MET cc_start: -0.4585 (ptm) cc_final: -0.4882 (ptp) REVERT: D 668 ASP cc_start: 0.9072 (p0) cc_final: 0.8643 (m-30) REVERT: D 755 GLU cc_start: 0.6004 (mt-10) cc_final: 0.5741 (pp20) REVERT: E 95 GLU cc_start: 0.8580 (mp0) cc_final: 0.8159 (mp0) REVERT: E 128 TYR cc_start: 0.7086 (t80) cc_final: 0.6831 (t80) REVERT: F 24 MET cc_start: 0.9211 (tpt) cc_final: 0.8929 (tpt) REVERT: F 61 SER cc_start: 0.8964 (t) cc_final: 0.8520 (p) REVERT: F 65 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7772 (mtm110) REVERT: F 67 CYS cc_start: 0.7166 (m) cc_final: 0.6274 (m) REVERT: F 81 ASP cc_start: 0.8455 (t0) cc_final: 0.8116 (t70) REVERT: G 81 ASP cc_start: 0.9012 (p0) cc_final: 0.8633 (t0) REVERT: G 102 ARG cc_start: 0.8879 (tpt90) cc_final: 0.8641 (tpt90) REVERT: H 35 TYR cc_start: 0.8865 (m-80) cc_final: 0.8553 (m-80) REVERT: H 61 SER cc_start: 0.9388 (t) cc_final: 0.8692 (p) REVERT: H 74 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8720 (ttmt) REVERT: H 81 ASP cc_start: 0.9168 (t0) cc_final: 0.8929 (t0) outliers start: 58 outliers final: 15 residues processed: 232 average time/residue: 1.2543 time to fit residues: 327.7112 Evaluate side-chains 194 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 158 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.154128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090845 restraints weight = 98026.970| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 7.11 r_work: 0.2977 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18592 Z= 0.137 Angle : 0.604 12.855 25062 Z= 0.308 Chirality : 0.042 0.295 2793 Planarity : 0.004 0.074 3050 Dihedral : 10.112 88.750 2828 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 2.57 % Allowed : 16.17 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.18), residues: 2268 helix: 2.60 (0.14), residues: 1342 sheet: -0.69 (0.39), residues: 146 loop : -1.03 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 671 HIS 0.005 0.001 HIS G 60 PHE 0.016 0.001 PHE H 73 TYR 0.020 0.001 TYR A 405 ARG 0.008 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1131) hydrogen bonds : angle 3.97619 ( 3272) SS BOND : bond 0.00645 ( 12) SS BOND : angle 2.01018 ( 24) covalent geometry : bond 0.00313 (18580) covalent geometry : angle 0.60117 (25038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 2.074 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 407 MET cc_start: 0.7582 (pmm) cc_final: 0.7379 (pmm) REVERT: A 408 MET cc_start: 0.7906 (mpt) cc_final: 0.6331 (mmt) REVERT: A 463 MET cc_start: 0.5514 (mtm) cc_final: 0.4744 (mpp) REVERT: A 496 MET cc_start: 0.6863 (tmm) cc_final: 0.5685 (tmm) REVERT: B 670 MET cc_start: 0.9306 (ptt) cc_final: 0.8809 (ptt) REVERT: B 714 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8628 (mm-40) REVERT: C 414 MET cc_start: 0.1823 (mtm) cc_final: 0.1546 (mtp) REVERT: C 585 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.7933 (mpt) REVERT: C 674 MET cc_start: -0.4498 (ptm) cc_final: -0.4897 (ptp) REVERT: D 401 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6355 (mp) REVERT: D 408 MET cc_start: 0.6322 (mpm) cc_final: 0.5805 (mpm) REVERT: D 463 MET cc_start: 0.5745 (mmt) cc_final: 0.5404 (mmp) REVERT: D 496 MET cc_start: 0.6525 (mmm) cc_final: 0.6170 (mtp) REVERT: D 503 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.5013 (tpt) REVERT: D 629 MET cc_start: 0.6450 (ppp) cc_final: 0.5941 (ppp) REVERT: D 668 ASP cc_start: 0.9094 (p0) cc_final: 0.8734 (m-30) REVERT: E 95 GLU cc_start: 0.8538 (mp0) cc_final: 0.8257 (mp0) REVERT: E 128 TYR cc_start: 0.7171 (t80) cc_final: 0.6879 (t80) REVERT: F 61 SER cc_start: 0.8909 (t) cc_final: 0.8423 (p) REVERT: F 65 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7816 (mtm110) REVERT: F 67 CYS cc_start: 0.7494 (m) cc_final: 0.6808 (m) REVERT: F 81 ASP cc_start: 0.8452 (t0) cc_final: 0.8105 (t70) REVERT: G 60 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.7880 (p90) REVERT: G 81 ASP cc_start: 0.8783 (p0) cc_final: 0.8534 (t0) REVERT: G 99 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8789 (tpp80) REVERT: G 102 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8485 (tpt90) REVERT: H 34 LEU cc_start: 0.9024 (tp) cc_final: 0.8396 (tp) REVERT: H 35 TYR cc_start: 0.8811 (m-80) cc_final: 0.8368 (m-80) REVERT: H 61 SER cc_start: 0.9298 (t) cc_final: 0.8452 (p) outliers start: 47 outliers final: 16 residues processed: 229 average time/residue: 1.4669 time to fit residues: 380.6687 Evaluate side-chains 199 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 16 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 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 = 0.4344 r_free = 0.4344 target = 0.153509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088511 restraints weight = 88479.677| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 6.65 r_work: 0.2955 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18592 Z= 0.147 Angle : 0.598 12.787 25062 Z= 0.306 Chirality : 0.042 0.231 2793 Planarity : 0.004 0.045 3050 Dihedral : 9.724 89.593 2828 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 3.06 % Allowed : 16.55 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2268 helix: 2.64 (0.14), residues: 1344 sheet: -0.91 (0.38), residues: 153 loop : -0.96 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 671 HIS 0.006 0.001 HIS G 60 PHE 0.024 0.001 PHE H 127 TYR 0.023 0.001 TYR A 768 ARG 0.010 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1131) hydrogen bonds : angle 3.96964 ( 3272) SS BOND : bond 0.00658 ( 12) SS BOND : angle 2.09851 ( 24) covalent geometry : bond 0.00339 (18580) covalent geometry : angle 0.59487 (25038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 2.319 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 408 MET cc_start: 0.7891 (mpt) cc_final: 0.6311 (mmt) REVERT: A 463 MET cc_start: 0.5748 (mtm) cc_final: 0.4922 (mpp) REVERT: A 493 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7384 (ptpt) REVERT: B 407 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7076 (mpp) REVERT: C 414 MET cc_start: 0.1959 (mtm) cc_final: 0.1667 (mtp) REVERT: C 585 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.7888 (mpt) REVERT: C 674 MET cc_start: -0.4509 (ptm) cc_final: -0.4929 (ptp) REVERT: C 695 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6492 (ptpp) REVERT: D 401 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6579 (mp) REVERT: D 408 MET cc_start: 0.6241 (mpm) cc_final: 0.5737 (mpm) REVERT: D 463 MET cc_start: 0.5827 (mmt) cc_final: 0.5531 (mmp) REVERT: D 496 MET cc_start: 0.6412 (mmm) cc_final: 0.5976 (mtp) REVERT: D 503 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5456 (tpp) REVERT: D 629 MET cc_start: 0.6661 (ppp) cc_final: 0.6196 (ppp) REVERT: D 668 ASP cc_start: 0.9107 (p0) cc_final: 0.8748 (m-30) REVERT: E 69 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6543 (pp) REVERT: E 95 GLU cc_start: 0.8569 (mp0) cc_final: 0.8199 (mp0) REVERT: E 128 TYR cc_start: 0.7215 (t80) cc_final: 0.6878 (t80) REVERT: E 135 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (pt) REVERT: F 10 MET cc_start: 0.8736 (tpp) cc_final: 0.8502 (tpt) REVERT: F 61 SER cc_start: 0.8940 (t) cc_final: 0.8467 (p) REVERT: F 65 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7840 (mtm180) REVERT: F 81 ASP cc_start: 0.8419 (t0) cc_final: 0.8095 (t70) REVERT: G 81 ASP cc_start: 0.8842 (p0) cc_final: 0.8542 (t0) REVERT: G 99 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8803 (tpp80) REVERT: G 102 ARG cc_start: 0.8776 (tpt90) cc_final: 0.8481 (tpt90) REVERT: G 126 GLU cc_start: 0.8855 (tt0) cc_final: 0.8334 (tp30) REVERT: G 205 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8019 (t-90) REVERT: H 34 LEU cc_start: 0.9007 (tp) cc_final: 0.8362 (tp) REVERT: H 35 TYR cc_start: 0.8820 (m-80) cc_final: 0.8355 (m-80) REVERT: H 61 SER cc_start: 0.9355 (t) cc_final: 0.8512 (p) REVERT: H 74 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8827 (ttmt) outliers start: 56 outliers final: 20 residues processed: 232 average time/residue: 1.2161 time to fit residues: 318.6652 Evaluate side-chains 209 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 210 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.151146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083971 restraints weight = 82562.803| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.79 r_work: 0.2920 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18592 Z= 0.229 Angle : 0.667 12.557 25062 Z= 0.341 Chirality : 0.044 0.196 2793 Planarity : 0.004 0.043 3050 Dihedral : 9.961 85.950 2828 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.79 % Favored : 97.03 % Rotamer: Outliers : 3.00 % Allowed : 17.37 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.18), residues: 2268 helix: 2.43 (0.14), residues: 1351 sheet: -1.03 (0.41), residues: 127 loop : -0.96 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 767 HIS 0.006 0.001 HIS D 412 PHE 0.031 0.002 PHE A 658 TYR 0.019 0.002 TYR C 647 ARG 0.010 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 1131) hydrogen bonds : angle 4.20918 ( 3272) SS BOND : bond 0.01085 ( 12) SS BOND : angle 2.56091 ( 24) covalent geometry : bond 0.00535 (18580) covalent geometry : angle 0.66222 (25038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 2.137 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: 0.7816 (mpt) cc_final: 0.6573 (mmt) REVERT: A 463 MET cc_start: 0.5741 (mtm) cc_final: 0.4958 (mpp) REVERT: A 493 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7623 (ptpt) REVERT: A 713 GLU cc_start: 0.9178 (tt0) cc_final: 0.8813 (tp30) REVERT: A 721 MET cc_start: 0.8361 (pp-130) cc_final: 0.8074 (ppp) REVERT: B 407 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7030 (mpp) REVERT: B 714 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8344 (mm-40) REVERT: C 414 MET cc_start: 0.2361 (mtm) cc_final: 0.2113 (mtp) REVERT: C 674 MET cc_start: -0.4207 (ptm) cc_final: -0.4574 (ptp) REVERT: C 695 LYS cc_start: 0.7173 (mmtm) cc_final: 0.6760 (pptt) REVERT: D 401 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6530 (mp) REVERT: D 408 MET cc_start: 0.6250 (mpm) cc_final: 0.5862 (mpm) REVERT: D 463 MET cc_start: 0.5820 (mmt) cc_final: 0.5588 (mmm) REVERT: D 496 MET cc_start: 0.6601 (mmm) cc_final: 0.6197 (mtp) REVERT: D 503 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5584 (tpp) REVERT: D 629 MET cc_start: 0.6766 (ppp) cc_final: 0.6259 (ppp) REVERT: D 668 ASP cc_start: 0.9100 (p0) cc_final: 0.8739 (m-30) REVERT: E 58 MET cc_start: 0.8305 (tpt) cc_final: 0.8098 (tpt) REVERT: E 95 GLU cc_start: 0.8552 (mp0) cc_final: 0.8267 (mp0) REVERT: E 128 TYR cc_start: 0.7305 (t80) cc_final: 0.6992 (t80) REVERT: F 61 SER cc_start: 0.9116 (t) cc_final: 0.8637 (p) REVERT: F 65 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.7811 (mtm180) REVERT: F 81 ASP cc_start: 0.8445 (t0) cc_final: 0.8121 (t70) REVERT: G 81 ASP cc_start: 0.8822 (p0) cc_final: 0.8503 (t0) REVERT: G 99 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8787 (tpp80) REVERT: G 102 ARG cc_start: 0.8932 (tpt90) cc_final: 0.8530 (tpt90) REVERT: G 126 GLU cc_start: 0.8879 (tt0) cc_final: 0.8381 (tp30) REVERT: G 205 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7953 (t-90) REVERT: H 35 TYR cc_start: 0.8877 (m-80) cc_final: 0.8468 (m-80) REVERT: H 61 SER cc_start: 0.9392 (t) cc_final: 0.8534 (p) REVERT: H 74 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8699 (ttmm) REVERT: H 205 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7439 (m-70) outliers start: 55 outliers final: 26 residues processed: 222 average time/residue: 1.4867 time to fit residues: 372.2162 Evaluate side-chains 209 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 63 optimal weight: 20.0000 chunk 55 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN D 412 HIS E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN G 205 HIS H 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.154200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088283 restraints weight = 73786.778| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.54 r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18592 Z= 0.125 Angle : 0.613 11.748 25062 Z= 0.310 Chirality : 0.042 0.227 2793 Planarity : 0.003 0.041 3050 Dihedral : 9.316 86.284 2828 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.87 % Rotamer: Outliers : 2.40 % Allowed : 17.97 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.18), residues: 2268 helix: 2.70 (0.14), residues: 1350 sheet: -0.82 (0.43), residues: 121 loop : -0.93 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 178 HIS 0.006 0.001 HIS G 60 PHE 0.029 0.001 PHE A 658 TYR 0.017 0.001 TYR C 647 ARG 0.008 0.000 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1131) hydrogen bonds : angle 3.97820 ( 3272) SS BOND : bond 0.00812 ( 12) SS BOND : angle 2.03485 ( 24) covalent geometry : bond 0.00279 (18580) covalent geometry : angle 0.61027 (25038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 1.946 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 407 MET cc_start: 0.7597 (pmm) cc_final: 0.7356 (pmm) REVERT: A 408 MET cc_start: 0.7862 (mpt) cc_final: 0.6434 (mmt) REVERT: A 463 MET cc_start: 0.5744 (mtm) cc_final: 0.5339 (mpp) REVERT: A 479 LEU cc_start: 0.8677 (tp) cc_final: 0.8086 (mm) REVERT: A 493 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7554 (mttm) REVERT: A 503 MET cc_start: 0.6941 (tpt) cc_final: 0.6044 (tpp) REVERT: A 587 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8783 (tp40) REVERT: A 713 GLU cc_start: 0.9317 (tt0) cc_final: 0.8967 (mm-30) REVERT: B 407 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6964 (mpp) REVERT: B 493 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6352 (tmtt) REVERT: B 768 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8105 (p90) REVERT: C 414 MET cc_start: 0.2415 (mtm) cc_final: 0.2154 (mtp) REVERT: C 585 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.7893 (mpt) REVERT: C 674 MET cc_start: -0.4191 (ptm) cc_final: -0.4544 (ptp) REVERT: C 695 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6805 (pptt) REVERT: D 408 MET cc_start: 0.6071 (mpm) cc_final: 0.5655 (mpp) REVERT: D 463 MET cc_start: 0.6053 (mmt) cc_final: 0.5768 (mmm) REVERT: D 496 MET cc_start: 0.6654 (mmm) cc_final: 0.6233 (mtp) REVERT: D 508 GLN cc_start: 0.8536 (pt0) cc_final: 0.7686 (pm20) REVERT: D 629 MET cc_start: 0.6999 (ppp) cc_final: 0.6750 (ppp) REVERT: D 668 ASP cc_start: 0.9117 (p0) cc_final: 0.8823 (m-30) REVERT: D 755 GLU cc_start: 0.6414 (mt-10) cc_final: 0.5841 (pp20) REVERT: E 58 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (tpt) REVERT: E 95 GLU cc_start: 0.8602 (mp0) cc_final: 0.8239 (mp0) REVERT: E 128 TYR cc_start: 0.7260 (t80) cc_final: 0.7001 (t80) REVERT: F 10 MET cc_start: 0.8806 (tpp) cc_final: 0.8571 (tpt) REVERT: F 61 SER cc_start: 0.8989 (t) cc_final: 0.8491 (p) REVERT: F 65 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.7724 (mtm110) REVERT: F 81 ASP cc_start: 0.8416 (t0) cc_final: 0.8098 (t70) REVERT: G 58 MET cc_start: 0.8716 (tpt) cc_final: 0.8267 (tpt) REVERT: G 99 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8843 (tpp80) REVERT: G 102 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8586 (tpt90) REVERT: G 126 GLU cc_start: 0.8853 (tt0) cc_final: 0.8393 (tp30) REVERT: H 35 TYR cc_start: 0.8811 (m-80) cc_final: 0.8395 (m-80) REVERT: H 61 SER cc_start: 0.9203 (t) cc_final: 0.8185 (p) REVERT: H 205 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7285 (m-70) outliers start: 44 outliers final: 17 residues processed: 228 average time/residue: 1.2682 time to fit residues: 327.9745 Evaluate side-chains 207 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 202 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 151 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 182 optimal weight: 0.0370 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.153852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083639 restraints weight = 74154.219| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.20 r_work: 0.3030 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18592 Z= 0.139 Angle : 0.650 16.967 25062 Z= 0.323 Chirality : 0.042 0.252 2793 Planarity : 0.004 0.050 3050 Dihedral : 9.166 87.676 2828 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.46 % Allowed : 18.57 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2268 helix: 2.71 (0.14), residues: 1351 sheet: -0.93 (0.41), residues: 130 loop : -0.97 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 460 HIS 0.005 0.001 HIS G 60 PHE 0.013 0.001 PHE A 584 TYR 0.016 0.001 TYR C 647 ARG 0.012 0.000 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 1131) hydrogen bonds : angle 3.98953 ( 3272) SS BOND : bond 0.00833 ( 12) SS BOND : angle 2.07714 ( 24) covalent geometry : bond 0.00318 (18580) covalent geometry : angle 0.64704 (25038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.995 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 408 MET cc_start: 0.7844 (mpt) cc_final: 0.6412 (mmt) REVERT: A 463 MET cc_start: 0.5755 (mtm) cc_final: 0.5391 (mpp) REVERT: A 479 LEU cc_start: 0.8670 (tp) cc_final: 0.8083 (mm) REVERT: A 493 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7708 (ptpt) REVERT: A 585 MET cc_start: 0.8796 (mpt) cc_final: 0.8352 (mpt) REVERT: A 587 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8747 (tp40) REVERT: A 713 GLU cc_start: 0.9350 (tt0) cc_final: 0.8903 (tp30) REVERT: B 407 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7074 (mpp) REVERT: B 768 TYR cc_start: 0.8174 (p90) cc_final: 0.7961 (p90) REVERT: C 414 MET cc_start: 0.2283 (mtm) cc_final: 0.2056 (mtp) REVERT: C 585 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.7897 (mpt) REVERT: C 674 MET cc_start: -0.4159 (ptm) cc_final: -0.4508 (ptp) REVERT: C 695 LYS cc_start: 0.7298 (mmtm) cc_final: 0.6986 (pptt) REVERT: D 463 MET cc_start: 0.6054 (mmt) cc_final: 0.5847 (mmm) REVERT: D 496 MET cc_start: 0.6225 (mmm) cc_final: 0.5772 (mtp) REVERT: D 503 MET cc_start: 0.5379 (tpp) cc_final: 0.5015 (tpt) REVERT: D 508 GLN cc_start: 0.8519 (pt0) cc_final: 0.7662 (pm20) REVERT: D 629 MET cc_start: 0.7014 (ppp) cc_final: 0.6530 (ppp) REVERT: D 668 ASP cc_start: 0.9112 (p0) cc_final: 0.8821 (m-30) REVERT: E 58 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: E 95 GLU cc_start: 0.8576 (mp0) cc_final: 0.8262 (mp0) REVERT: E 128 TYR cc_start: 0.7234 (t80) cc_final: 0.6934 (t80) REVERT: F 10 MET cc_start: 0.8844 (tpp) cc_final: 0.8624 (tpt) REVERT: F 61 SER cc_start: 0.8969 (t) cc_final: 0.8480 (p) REVERT: F 65 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7717 (mtm180) REVERT: F 81 ASP cc_start: 0.8432 (t0) cc_final: 0.8080 (t0) REVERT: G 58 MET cc_start: 0.8626 (tpt) cc_final: 0.8225 (tpt) REVERT: G 99 ARG cc_start: 0.9238 (tpp80) cc_final: 0.8680 (tpp80) REVERT: G 102 ARG cc_start: 0.8787 (tpt90) cc_final: 0.8547 (tpt90) REVERT: G 126 GLU cc_start: 0.8858 (tt0) cc_final: 0.8406 (tp30) REVERT: H 35 TYR cc_start: 0.8805 (m-80) cc_final: 0.8400 (m-80) REVERT: H 61 SER cc_start: 0.9228 (t) cc_final: 0.8198 (p) REVERT: H 74 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8618 (ttmm) REVERT: H 205 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7269 (m-70) outliers start: 45 outliers final: 20 residues processed: 223 average time/residue: 1.2448 time to fit residues: 314.3544 Evaluate side-chains 204 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 41 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.154432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084351 restraints weight = 78329.742| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.52 r_work: 0.3054 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18592 Z= 0.134 Angle : 0.657 13.872 25062 Z= 0.324 Chirality : 0.042 0.246 2793 Planarity : 0.004 0.047 3050 Dihedral : 8.895 89.527 2828 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.87 % Rotamer: Outliers : 2.08 % Allowed : 19.28 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2268 helix: 2.74 (0.14), residues: 1351 sheet: -1.05 (0.41), residues: 135 loop : -0.90 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 178 HIS 0.005 0.001 HIS G 60 PHE 0.027 0.001 PHE H 127 TYR 0.019 0.001 TYR A 768 ARG 0.012 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1131) hydrogen bonds : angle 3.93648 ( 3272) SS BOND : bond 0.00804 ( 12) SS BOND : angle 1.91503 ( 24) covalent geometry : bond 0.00306 (18580) covalent geometry : angle 0.65431 (25038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.892 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 408 MET cc_start: 0.7842 (mpt) cc_final: 0.6449 (mmt) REVERT: A 463 MET cc_start: 0.5787 (mtm) cc_final: 0.5395 (mpp) REVERT: A 479 LEU cc_start: 0.8652 (tp) cc_final: 0.8086 (mm) REVERT: A 493 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7726 (ptpt) REVERT: A 496 MET cc_start: 0.6840 (tmm) cc_final: 0.6020 (tmm) REVERT: A 587 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: A 713 GLU cc_start: 0.9336 (tt0) cc_final: 0.8912 (tp30) REVERT: B 453 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7468 (ptp90) REVERT: B 768 TYR cc_start: 0.8091 (p90) cc_final: 0.7810 (p90) REVERT: C 414 MET cc_start: 0.2268 (mtm) cc_final: 0.2042 (mtp) REVERT: C 585 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.7788 (mpt) REVERT: C 674 MET cc_start: -0.3964 (ptm) cc_final: -0.4260 (ptp) REVERT: C 695 LYS cc_start: 0.7320 (mmtm) cc_final: 0.7019 (pptt) REVERT: D 463 MET cc_start: 0.5909 (mmt) cc_final: 0.5678 (mmm) REVERT: D 496 MET cc_start: 0.6203 (mmm) cc_final: 0.5746 (mtp) REVERT: D 508 GLN cc_start: 0.8476 (pt0) cc_final: 0.7693 (pm20) REVERT: D 668 ASP cc_start: 0.9111 (p0) cc_final: 0.8814 (m-30) REVERT: E 95 GLU cc_start: 0.8634 (mp0) cc_final: 0.8401 (mp0) REVERT: E 128 TYR cc_start: 0.7234 (t80) cc_final: 0.6898 (t80) REVERT: F 10 MET cc_start: 0.8885 (tpp) cc_final: 0.8662 (tpt) REVERT: F 61 SER cc_start: 0.8984 (t) cc_final: 0.8532 (p) REVERT: F 65 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.7781 (mtm180) REVERT: F 81 ASP cc_start: 0.8390 (t0) cc_final: 0.8053 (t0) REVERT: G 58 MET cc_start: 0.8605 (tpt) cc_final: 0.8213 (tpt) REVERT: G 99 ARG cc_start: 0.9260 (tpp80) cc_final: 0.8707 (tpp80) REVERT: G 102 ARG cc_start: 0.8828 (tpt90) cc_final: 0.8627 (tpt90) REVERT: G 126 GLU cc_start: 0.8846 (tt0) cc_final: 0.8406 (tp30) REVERT: G 176 TYR cc_start: 0.9450 (m-80) cc_final: 0.9250 (m-80) REVERT: H 34 LEU cc_start: 0.8979 (tp) cc_final: 0.8352 (tp) REVERT: H 61 SER cc_start: 0.9190 (t) cc_final: 0.8167 (p) REVERT: H 74 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8582 (ttmm) REVERT: H 205 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7378 (m-70) outliers start: 38 outliers final: 23 residues processed: 222 average time/residue: 1.2452 time to fit residues: 311.2615 Evaluate side-chains 208 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 24 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.151594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084363 restraints weight = 88739.209| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 5.64 r_work: 0.2945 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18592 Z= 0.232 Angle : 0.718 13.813 25062 Z= 0.359 Chirality : 0.044 0.228 2793 Planarity : 0.004 0.050 3050 Dihedral : 9.361 89.641 2828 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 19.44 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2268 helix: 2.51 (0.14), residues: 1355 sheet: -1.18 (0.40), residues: 145 loop : -0.93 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 460 HIS 0.005 0.001 HIS E 132 PHE 0.015 0.002 PHE H 107 TYR 0.015 0.001 TYR C 647 ARG 0.014 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1131) hydrogen bonds : angle 4.15941 ( 3272) SS BOND : bond 0.00736 ( 12) SS BOND : angle 1.87108 ( 24) covalent geometry : bond 0.00543 (18580) covalent geometry : angle 0.71590 (25038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 2.162 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 408 MET cc_start: 0.7924 (mpt) cc_final: 0.6570 (mmt) REVERT: A 463 MET cc_start: 0.5545 (mtm) cc_final: 0.5009 (mpp) REVERT: A 479 LEU cc_start: 0.8641 (tp) cc_final: 0.8246 (mm) REVERT: A 496 MET cc_start: 0.6861 (tmm) cc_final: 0.5856 (tmm) REVERT: B 768 TYR cc_start: 0.8152 (p90) cc_final: 0.7841 (p90) REVERT: C 414 MET cc_start: 0.2408 (mtm) cc_final: 0.2169 (mtp) REVERT: C 585 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.7711 (mpt) REVERT: C 674 MET cc_start: -0.3721 (ptm) cc_final: -0.3929 (ptp) REVERT: C 695 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6852 (pptt) REVERT: D 463 MET cc_start: 0.6187 (mmt) cc_final: 0.5840 (mmm) REVERT: D 496 MET cc_start: 0.6803 (mmm) cc_final: 0.6341 (mtp) REVERT: D 508 GLN cc_start: 0.8587 (pt0) cc_final: 0.7744 (pm20) REVERT: D 668 ASP cc_start: 0.9044 (p0) cc_final: 0.8802 (m-30) REVERT: E 95 GLU cc_start: 0.8662 (mp0) cc_final: 0.8370 (mp0) REVERT: E 128 TYR cc_start: 0.7360 (t80) cc_final: 0.7059 (t80) REVERT: F 61 SER cc_start: 0.9110 (t) cc_final: 0.8678 (p) REVERT: F 65 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.7858 (mtm180) REVERT: F 81 ASP cc_start: 0.8485 (t0) cc_final: 0.8173 (t70) REVERT: G 58 MET cc_start: 0.8627 (tpt) cc_final: 0.8152 (tpt) REVERT: G 99 ARG cc_start: 0.9333 (tpp80) cc_final: 0.8799 (tpp80) REVERT: G 102 ARG cc_start: 0.9017 (tpt90) cc_final: 0.8767 (tpt90) REVERT: G 126 GLU cc_start: 0.8872 (tt0) cc_final: 0.8437 (tp30) REVERT: H 61 SER cc_start: 0.9444 (t) cc_final: 0.8798 (p) REVERT: H 74 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8720 (ttmm) outliers start: 35 outliers final: 25 residues processed: 205 average time/residue: 1.3735 time to fit residues: 322.3569 Evaluate side-chains 196 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 5 optimal weight: 20.0000 chunk 133 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.153930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089031 restraints weight = 85842.879| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 5.78 r_work: 0.3001 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18592 Z= 0.134 Angle : 0.681 13.784 25062 Z= 0.338 Chirality : 0.042 0.197 2793 Planarity : 0.004 0.042 3050 Dihedral : 9.051 87.953 2828 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.82 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 19.72 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2268 helix: 2.66 (0.14), residues: 1354 sheet: -1.01 (0.40), residues: 139 loop : -0.95 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 671 HIS 0.004 0.001 HIS G 60 PHE 0.028 0.001 PHE H 127 TYR 0.032 0.001 TYR A 768 ARG 0.011 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 1131) hydrogen bonds : angle 3.99100 ( 3272) SS BOND : bond 0.00704 ( 12) SS BOND : angle 1.40934 ( 24) covalent geometry : bond 0.00304 (18580) covalent geometry : angle 0.68038 (25038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17740.41 seconds wall clock time: 306 minutes 0.60 seconds (18360.60 seconds total)