Starting phenix.real_space_refine on Tue Oct 27 08:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uh5_20767/10_2026/6uh5_20767.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 79 5.16 5 C 14533 2.51 5 N 4361 2.21 5 O 5200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24466 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 722 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2365 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1775 Classifications: {'peptide': 222} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 2 Chain: "N" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3273 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 63 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "X" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 604 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Chain: "L" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3128 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "P" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 329 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16028 SG CYS M 988 100.644 72.149 42.184 1.00142.90 S ATOM 16042 SG CYS M 990 95.749 71.558 42.382 1.00156.46 S ATOM 16070 SG CYS M 995 98.805 74.904 40.292 1.00160.65 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET R 4 " occ=0.84 ... (6 atoms not shown) pdb=" CE MET R 4 " occ=0.84 residue: pdb="ZN ZN M1101 " occ=0.41 Time building chain proxies: 5.47, per 1000 atoms: 0.22 Number of scatterers: 24466 At special positions: 0 Unit cell: (174.24, 134.112, 130.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 79 16.00 P 292 15.00 O 5200 8.00 N 4361 7.00 C 14533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS Q 76 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M1101 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 995 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 988 " pdb="ZN ZN M1101 " - pdb=" SG CYS M 990 " 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 35 sheets defined 33.6% alpha, 15.7% beta 131 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.075A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.078A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.607A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.583A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.923A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.672A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.684A pdb=" N LEU C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.799A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.693A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.840A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 77 removed outlier: 3.901A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.724A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.568A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.956A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.831A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 114 removed outlier: 3.979A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.179A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 52 removed outlier: 3.823A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 53 through 77 removed outlier: 3.619A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.727A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.527A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.717A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.749A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 Processing helix chain 'H' and resid 56 through 81 removed outlier: 3.643A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.685A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 739 removed outlier: 4.043A pdb=" N ILE M 735 " --> pdb=" O GLN M 731 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN M 738 " --> pdb=" O ILE M 734 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN M 739 " --> pdb=" O ILE M 735 " (cutoff:3.500A) Processing helix chain 'M' and resid 820 through 832 removed outlier: 3.509A pdb=" N PHE M 830 " --> pdb=" O PHE M 826 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN M 831 " --> pdb=" O GLN M 827 " (cutoff:3.500A) Processing helix chain 'M' and resid 894 through 907 removed outlier: 3.864A pdb=" N ILE M 905 " --> pdb=" O GLU M 901 " (cutoff:3.500A) Processing helix chain 'M' and resid 930 through 935 removed outlier: 3.675A pdb=" N ARG M 933 " --> pdb=" O GLY M 930 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE M 935 " --> pdb=" O ALA M 932 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 8 removed outlier: 3.896A pdb=" N GLN N 7 " --> pdb=" O ASN N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 359 Processing helix chain 'N' and resid 427 through 432 removed outlier: 3.786A pdb=" N GLN N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 35 Processing helix chain 'Q' and resid 37 through 41 Processing helix chain 'X' and resid 200 through 211 removed outlier: 4.058A pdb=" N VAL X 205 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL X 210 " --> pdb=" O ILE X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 219 Processing helix chain 'X' and resid 221 through 226 removed outlier: 4.025A pdb=" N GLN X 226 " --> pdb=" O HIS X 223 " (cutoff:3.500A) Processing helix chain 'X' and resid 294 through 308 removed outlier: 4.353A pdb=" N LEU X 298 " --> pdb=" O SER X 294 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU X 300 " --> pdb=" O ASN X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 308 through 313 Processing helix chain 'X' and resid 317 through 325 removed outlier: 3.648A pdb=" N ASN X 321 " --> pdb=" O SER X 317 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE X 325 " --> pdb=" O ASN X 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 211 removed outlier: 3.555A pdb=" N GLN L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLN L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 237 Processing helix chain 'L' and resid 367 through 371 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.801A pdb=" N ILE L 386 " --> pdb=" O THR L 382 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 387 " --> pdb=" O LEU L 383 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE L 395 " --> pdb=" O ILE L 391 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 95 removed outlier: 3.514A pdb=" N TYR O 90 " --> pdb=" O THR O 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 107 removed outlier: 3.684A pdb=" N ILE O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA O 107 " --> pdb=" O MET O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 126 removed outlier: 3.984A pdb=" N VAL O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 122 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA O 125 " --> pdb=" O PHE O 121 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 84 removed outlier: 3.619A pdb=" N GLY P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 89 Processing helix chain 'P' and resid 90 through 95 Processing helix chain 'P' and resid 95 through 104 Processing helix chain 'P' and resid 114 through 121 removed outlier: 4.111A pdb=" N LEU P 118 " --> pdb=" O PRO P 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.680A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.164A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.237A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 18 through 22 removed outlier: 5.653A pdb=" N PHE K 19 " --> pdb=" O ARG K 325 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG K 325 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 21 " --> pdb=" O LEU K 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 31 through 36 removed outlier: 3.750A pdb=" N ASP K 50 " --> pdb=" O GLN K 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 76 through 77 removed outlier: 3.699A pdb=" N CYS K 76 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA K 85 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL K 93 " --> pdb=" O ARG K 105 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG K 105 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE K 95 " --> pdb=" O ILE K 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 116 through 117 removed outlier: 3.660A pdb=" N LEU K 125 " --> pdb=" O TRP K 137 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP K 137 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS K 146 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS K 138 " --> pdb=" O ALA K 144 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA K 144 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 157 through 159 removed outlier: 3.578A pdb=" N SER K 157 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE K 177 " --> pdb=" O THR K 190 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR K 190 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE K 179 " --> pdb=" O LEU K 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 206 through 211 removed outlier: 6.756A pdb=" N LYS K 221 " --> pdb=" O SER K 207 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL K 209 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU K 219 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 239 " --> pdb=" O LEU K 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 258 through 260 removed outlier: 3.942A pdb=" N SER K 272 " --> pdb=" O CYS K 280 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS K 280 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN K 291 " --> pdb=" O VAL K 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 305 through 306 removed outlier: 3.786A pdb=" N SER K 306 " --> pdb=" O ALA K 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 861 through 864 removed outlier: 3.751A pdb=" N GLU M 968 " --> pdb=" O ALA M 874 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 885 through 887 removed outlier: 3.966A pdb=" N ILE M 885 " --> pdb=" O ILE M 958 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE M 956 " --> pdb=" O TYR M 887 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG M 953 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 890 through 893 removed outlier: 3.888A pdb=" N ASP M 918 " --> pdb=" O THR M 921 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE M 923 " --> pdb=" O ARG M 916 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG M 916 " --> pdb=" O ILE M 923 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 19 through 24 removed outlier: 4.046A pdb=" N LYS N 19 " --> pdb=" O SER N 349 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET N 347 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR N 23 " --> pdb=" O VAL N 345 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL N 345 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP N 325 " --> pdb=" O ASN N 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 30 through 35 removed outlier: 6.483A pdb=" N ILE N 51 " --> pdb=" O MET N 64 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N MET N 64 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE N 53 " --> pdb=" O ILE N 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 76 through 81 removed outlier: 7.144A pdb=" N LEU N 99 " --> pdb=" O PHE N 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 118 through 123 removed outlier: 4.492A pdb=" N SER N 120 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 132 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL N 131 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR N 140 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE N 154 " --> pdb=" O VAL N 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR N 143 " --> pdb=" O HIS N 152 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS N 152 " --> pdb=" O THR N 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 171 through 174 removed outlier: 3.746A pdb=" N VAL N 171 " --> pdb=" O GLY N 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 183 " --> pdb=" O CYS N 173 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA N 193 " --> pdb=" O CYS N 209 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG N 207 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 221 through 224 removed outlier: 3.780A pdb=" N GLN N 221 " --> pdb=" O ASN N 234 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE N 231 " --> pdb=" O TYR N 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS N 266 " --> pdb=" O GLN N 242 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN N 244 " --> pdb=" O LEU N 264 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU N 264 " --> pdb=" O GLN N 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 246 through 247 Processing sheet with id=AC8, first strand: chain 'N' and resid 277 through 282 removed outlier: 6.595A pdb=" N SER N 293 " --> pdb=" O ASN N 278 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE N 280 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL N 291 " --> pdb=" O ILE N 280 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE N 282 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR N 289 " --> pdb=" O PHE N 282 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU N 302 " --> pdb=" O LEU N 316 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG N 314 " --> pdb=" O LEU N 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU N 306 " --> pdb=" O LEU N 312 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU N 312 " --> pdb=" O GLU N 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 2 through 3 Processing sheet with id=AD1, first strand: chain 'Q' and resid 48 through 50 removed outlier: 4.830A pdb=" N LEU Q 43 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 28 through 34 removed outlier: 7.011A pdb=" N TYR L 39 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG L 33 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 52 through 55 removed outlier: 3.811A pdb=" N ILE L 249 " --> pdb=" O GLU L 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD5, first strand: chain 'L' and resid 88 through 90 removed outlier: 5.927A pdb=" N PHE L 290 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE L 301 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL L 292 " --> pdb=" O HIS L 299 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 88 through 90 removed outlier: 3.719A pdb=" N LEU L 190 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE L 119 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS L 118 " --> pdb=" O LYS L 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 108 through 114 removed outlier: 3.934A pdb=" N ALA L 352 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL L 112 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR L 350 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER L 139 " --> pdb=" O TYR L 351 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 271 through 274 removed outlier: 4.066A pdb=" N ASP L 274 " --> pdb=" O MET L 279 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET L 279 " --> pdb=" O ASP L 274 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4078 1.32 - 1.45: 8645 1.45 - 1.58: 12124 1.58 - 1.71: 559 1.71 - 1.84: 119 Bond restraints: 25525 Sorted by residual: bond pdb=" C3' DG I 40 " pdb=" O3' DG I 40 " ideal model delta sigma weight residual 1.435 1.363 0.072 1.30e-02 5.92e+03 3.04e+01 bond pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " ideal model delta sigma weight residual 1.435 1.366 0.069 1.30e-02 5.92e+03 2.80e+01 bond pdb=" C3' DT I 58 " pdb=" O3' DT I 58 " ideal model delta sigma weight residual 1.435 1.369 0.066 1.30e-02 5.92e+03 2.56e+01 bond pdb=" CA THR E 118 " pdb=" CB THR E 118 " ideal model delta sigma weight residual 1.530 1.456 0.073 1.57e-02 4.06e+03 2.19e+01 bond pdb=" N7 DA J 91 " pdb=" C5 DA J 91 " ideal model delta sigma weight residual 1.388 1.360 0.028 6.00e-03 2.78e+04 2.14e+01 ... (remaining 25520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.42: 35613 7.42 - 14.85: 124 14.85 - 22.27: 17 22.27 - 29.69: 5 29.69 - 37.12: 3 Bond angle restraints: 35762 Sorted by residual: angle pdb=" N LYS M 857 " pdb=" CA LYS M 857 " pdb=" C LYS M 857 " ideal model delta sigma weight residual 111.07 141.71 -30.64 1.07e+00 8.73e-01 8.20e+02 angle pdb=" N ARG L 237 " pdb=" CA ARG L 237 " pdb=" C ARG L 237 " ideal model delta sigma weight residual 110.59 73.97 36.62 1.45e+00 4.76e-01 6.38e+02 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 112.93 140.59 -27.66 1.12e+00 7.97e-01 6.10e+02 angle pdb=" N ARG F 95 " pdb=" CA ARG F 95 " pdb=" C ARG F 95 " ideal model delta sigma weight residual 108.69 71.57 37.12 1.77e+00 3.19e-01 4.40e+02 angle pdb=" N GLY M 952 " pdb=" CA GLY M 952 " pdb=" C GLY M 952 " ideal model delta sigma weight residual 115.30 143.94 -28.64 1.44e+00 4.82e-01 3.96e+02 ... (remaining 35757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 12913 35.43 - 70.87: 1633 70.87 - 106.30: 40 106.30 - 141.74: 1 141.74 - 177.17: 2 Dihedral angle restraints: 14589 sinusoidal: 7832 harmonic: 6757 Sorted by residual: dihedral pdb=" C LEU Q 8 " pdb=" N LEU Q 8 " pdb=" CA LEU Q 8 " pdb=" CB LEU Q 8 " ideal model delta harmonic sigma weight residual -122.60 -158.44 35.84 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N LEU Q 8 " pdb=" C LEU Q 8 " pdb=" CA LEU Q 8 " pdb=" CB LEU Q 8 " ideal model delta harmonic sigma weight residual 122.80 155.81 -33.01 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" N SER L 238 " pdb=" C SER L 238 " pdb=" CA SER L 238 " pdb=" CB SER L 238 " ideal model delta harmonic sigma weight residual 122.80 154.95 -32.15 0 2.50e+00 1.60e-01 1.65e+02 ... (remaining 14586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 4003 0.309 - 0.617: 26 0.617 - 0.926: 7 0.926 - 1.234: 1 1.234 - 1.543: 3 Chirality restraints: 4040 Sorted by residual: chirality pdb=" CA LEU Q 8 " pdb=" N LEU Q 8 " pdb=" C LEU Q 8 " pdb=" CB LEU Q 8 " both_signs ideal model delta sigma weight residual False 2.51 0.97 1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" CA MET N 56 " pdb=" N MET N 56 " pdb=" C MET N 56 " pdb=" CB MET N 56 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.28e+01 chirality pdb=" CA SER L 238 " pdb=" N SER L 238 " pdb=" C SER L 238 " pdb=" CB SER L 238 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.91e+01 ... (remaining 4037 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 310 " 0.059 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO L 311 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO L 311 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 311 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS M 857 " -0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS M 857 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS M 857 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS M 858 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 884 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE M 884 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE M 884 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE M 885 " 0.019 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 78 2.38 - 3.01: 12367 3.01 - 3.64: 39652 3.64 - 4.27: 61107 4.27 - 4.90: 93782 Nonbonded interactions: 206986 Sorted by model distance: nonbonded pdb=" O LEU F 90 " pdb=" O ARG F 95 " model vdw 1.749 3.040 nonbonded pdb=" N ARG L 237 " pdb=" O ARG L 237 " model vdw 1.782 2.496 nonbonded pdb=" N ARG F 95 " pdb=" O ARG F 95 " model vdw 2.000 2.496 nonbonded pdb=" OE1 GLU N 368 " pdb=" NZ LYS Q 11 " model vdw 2.073 3.120 nonbonded pdb=" O ILE K 198 " pdb=" O SER M 907 " model vdw 2.120 3.040 ... (remaining 206981 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = (chain 'D' and (resid 29 through 116 or resid 118 through 121)) selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 116 or resid 118 through 121)) } ncs_group { reference = (chain 'O' and (resid 85 through 106 or resid 113 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 126)) selection = (chain 'P' and resid 85 through 126) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.617 25530 Z= 0.771 Angle : 1.439 37.118 35764 Z= 0.959 Chirality : 0.092 1.543 4040 Planarity : 0.007 0.087 3532 Dihedral : 23.784 177.172 10216 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 2.23 % Allowed : 11.61 % Favored : 86.16 % Cbeta Deviations : 1.74 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 1.25 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.14), residues: 2266 helix: -3.74 (0.12), residues: 732 sheet: -2.73 (0.23), residues: 364 loop : -2.80 (0.15), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG G 71 TYR 0.036 0.004 TYR H 34 PHE 0.033 0.003 PHE L 153 TRP 0.024 0.003 TRP N 95 HIS 0.018 0.003 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.75 (25525) covalent geometry : angle 1.43931 / 0.96 (35762) SS BOND : bond 0.01138 / 0.60 ( 1) SS BOND : angle 2.44313 / 1.43 ( 2) hydrogen bonds : bond 0.30076 / 20.11 ( 940) hydrogen bonds : angle 10.51608 / 7.38 ( 2373) metal coordination : bond 0.50052 / 25.04 ( 3) Misc. bond : bond 0.00517 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9003 (tp40) cc_final: 0.8738 (tp-100) REVERT: E 49 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8219 (ttm-80) REVERT: H 59 MET cc_start: 0.8905 (mmm) cc_final: 0.8601 (mmt) REVERT: K 118 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: K 194 ASP cc_start: 0.7214 (p0) cc_final: 0.6805 (t70) REVERT: M 831 GLN cc_start: 0.7115 (mp10) cc_final: 0.6457 (pp30) REVERT: M 857 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7041 (tttt) REVERT: N 44 VAL cc_start: 0.8866 (t) cc_final: 0.8580 (p) REVERT: N 64 MET cc_start: 0.7966 (ttt) cc_final: 0.7755 (tmm) REVERT: N 238 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6785 (mpp80) REVERT: N 364 GLU cc_start: 0.7791 (tp30) cc_final: 0.7563 (mm-30) REVERT: Q 13 ILE cc_start: 0.3453 (OUTLIER) cc_final: 0.3181 (tt) REVERT: R 2 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7402 (mpt180) REVERT: X 207 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7877 (tm-30) REVERT: L 53 MET cc_start: 0.5173 (ptp) cc_final: 0.4425 (tmm) REVERT: L 62 MET cc_start: 0.5340 (mpp) cc_final: 0.4731 (pmm) REVERT: L 68 TYR cc_start: 0.3726 (m-80) cc_final: 0.3452 (m-80) REVERT: L 144 SER cc_start: 0.6934 (m) cc_final: 0.6686 (p) REVERT: O 103 MET cc_start: 0.5514 (tpt) cc_final: 0.5116 (tpt) REVERT: O 106 ILE cc_start: 0.7753 (pt) cc_final: 0.7476 (tp) REVERT: O 121 PHE cc_start: 0.7214 (t80) cc_final: 0.6798 (t80) REVERT: O 122 LEU cc_start: 0.7787 (mp) cc_final: 0.7531 (mt) REVERT: P 88 ARG cc_start: 0.6148 (mmt90) cc_final: 0.5650 (ttp-170) outliers start: 45 outliers final: 10 residues processed: 306 average time/residue: 0.2074 time to fit residues: 93.6226 Evaluate side-chains 175 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 857 LYS Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 921 THR Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 352 ILE Chi-restraints excluded: chain Q residue 13 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain O residue 86 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 73 ASN C 112 GLN D 81 ASN E 68 GLN E 113 HIS F 25 ASN G 24 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS K 73 ASN K 288 ASN M 743 ASN M 827 GLN M 852 GLN N 7 GLN N 149 ASN N 175 HIS ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 GLN N 273 ASN N 412 ASN Q 68 HIS L 55 GLN L 133 HIS L 172 HIS L 181 GLN L 255 ASN L 317 GLN L 325 HIS L 344 ASN L 346 ASN ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.097902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066790 restraints weight = 94852.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.067862 restraints weight = 52042.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067340 restraints weight = 34147.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.067739 restraints weight = 40420.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067654 restraints weight = 33238.754| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25530 Z= 0.298 Angle : 0.871 12.757 35764 Z= 0.464 Chirality : 0.055 0.373 4040 Planarity : 0.006 0.070 3532 Dihedral : 27.635 175.410 5742 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 3.37 % Allowed : 15.97 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2266 helix: -2.31 (0.15), residues: 754 sheet: -2.25 (0.23), residues: 368 loop : -2.42 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 104 TYR 0.026 0.002 TYR M 972 PHE 0.027 0.002 PHE O 121 TRP 0.013 0.002 TRP K 137 HIS 0.013 0.002 HIS Q 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.30 (25525) covalent geometry : angle 0.87021 / 0.46 (35762) SS BOND : bond 0.02083 / 1.10 ( 1) SS BOND : angle 3.89535 / 2.25 ( 2) hydrogen bonds : bond 0.07651 / 4.96 ( 940) hydrogen bonds : angle 5.84136 / 4.08 ( 2373) metal coordination : bond 0.01219 / 0.61 ( 3) Misc. bond : bond 0.00294 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8321 (m-80) cc_final: 0.7974 (m-80) REVERT: E 49 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8389 (ttm-80) REVERT: F 44 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8810 (mtpp) REVERT: K 118 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.6227 (m-10) REVERT: K 194 ASP cc_start: 0.7323 (p0) cc_final: 0.6954 (t70) REVERT: K 234 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7878 (mmm160) REVERT: M 831 GLN cc_start: 0.6890 (mp10) cc_final: 0.6356 (pp30) REVERT: M 931 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8729 (tt) REVERT: N 44 VAL cc_start: 0.8700 (t) cc_final: 0.8461 (p) REVERT: N 64 MET cc_start: 0.7951 (ttt) cc_final: 0.7719 (tmm) REVERT: R 2 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7326 (mpt180) REVERT: X 207 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7771 (tm-30) REVERT: L 62 MET cc_start: 0.6025 (mpp) cc_final: 0.5683 (mmt) REVERT: L 124 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: L 144 SER cc_start: 0.7410 (m) cc_final: 0.7097 (p) REVERT: O 103 MET cc_start: 0.5934 (tpt) cc_final: 0.5396 (tpt) REVERT: O 106 ILE cc_start: 0.7375 (pt) cc_final: 0.7103 (tp) REVERT: O 121 PHE cc_start: 0.7674 (t80) cc_final: 0.7042 (t80) REVERT: O 122 LEU cc_start: 0.7817 (mp) cc_final: 0.7584 (mt) outliers start: 68 outliers final: 31 residues processed: 241 average time/residue: 0.1666 time to fit residues: 63.0321 Evaluate side-chains 189 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 124 GLU Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [247, 151, 250, 77, 59, 162, 139, 40, 213, 34, 200] chunk 247 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 213 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 200 optimal weight: 0.0070 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 81 ASN K 68 HIS N 175 HIS ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 ASN L 325 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.098408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068350 restraints weight = 95097.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.069755 restraints weight = 56169.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069314 restraints weight = 37159.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069777 restraints weight = 38150.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069681 restraints weight = 33039.634| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25530 Z= 0.149 Angle : 0.692 8.508 35764 Z= 0.382 Chirality : 0.048 0.362 4040 Planarity : 0.005 0.061 3532 Dihedral : 27.140 178.265 5731 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.88 % Allowed : 17.91 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.16), residues: 2266 helix: -1.29 (0.17), residues: 738 sheet: -2.02 (0.25), residues: 355 loop : -2.11 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 74 TYR 0.025 0.002 TYR H 80 PHE 0.015 0.001 PHE L 293 TRP 0.009 0.001 TRP K 137 HIS 0.008 0.001 HIS L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (25525) covalent geometry : angle 0.69152 / 0.38 (35762) SS BOND : bond 0.02002 / 1.05 ( 1) SS BOND : angle 1.08445 / 0.60 ( 2) hydrogen bonds : bond 0.06610 / 4.30 ( 940) hydrogen bonds : angle 5.14049 / 3.62 ( 2373) metal coordination : bond 0.01672 / 0.83 ( 3) Misc. bond : bond 0.01249 / 0.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.602 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: C 84 GLN cc_start: 0.9091 (tp40) cc_final: 0.8774 (tp-100) REVERT: E 41 TYR cc_start: 0.8212 (m-80) cc_final: 0.7967 (m-80) REVERT: K 118 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.6072 (m-10) REVERT: K 194 ASP cc_start: 0.7320 (p0) cc_final: 0.6949 (t70) REVERT: M 931 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8574 (tt) REVERT: N 44 VAL cc_start: 0.8557 (t) cc_final: 0.8268 (p) REVERT: N 64 MET cc_start: 0.7983 (ttt) cc_final: 0.7569 (tmm) REVERT: N 364 GLU cc_start: 0.7753 (tp30) cc_final: 0.7507 (mm-30) REVERT: L 144 SER cc_start: 0.7305 (m) cc_final: 0.7045 (p) REVERT: L 254 LYS cc_start: 0.8151 (mptp) cc_final: 0.7762 (tptt) REVERT: O 103 MET cc_start: 0.6039 (tpt) cc_final: 0.5565 (tpt) REVERT: O 121 PHE cc_start: 0.8016 (t80) cc_final: 0.7156 (t80) REVERT: O 122 LEU cc_start: 0.7848 (mp) cc_final: 0.7545 (mp) REVERT: P 99 LEU cc_start: 0.7578 (mt) cc_final: 0.7228 (pp) outliers start: 58 outliers final: 31 residues processed: 235 average time/residue: 0.1619 time to fit residues: 60.5592 Evaluate side-chains 183 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [244, 196, 45, 174, 37, 85, 222, 6, 239, 90, 207] chunk 244 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 HIS K 138 HIS ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 ASN L 228 ASN L 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065386 restraints weight = 93753.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066470 restraints weight = 53749.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066946 restraints weight = 36356.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067129 restraints weight = 32177.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067002 restraints weight = 28105.178| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 25530 Z= 0.315 Angle : 0.810 11.484 35764 Z= 0.427 Chirality : 0.051 0.386 4040 Planarity : 0.005 0.066 3532 Dihedral : 27.298 175.612 5730 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 4.27 % Allowed : 18.95 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 1.25 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2266 helix: -1.14 (0.18), residues: 733 sheet: -1.84 (0.25), residues: 363 loop : -2.10 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 95 TYR 0.023 0.002 TYR G 57 PHE 0.016 0.002 PHE L 293 TRP 0.011 0.002 TRP N 348 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.31 (25525) covalent geometry : angle 0.81022 / 0.43 (35762) SS BOND : bond 0.03335 / 1.76 ( 1) SS BOND : angle 2.38633 / 1.40 ( 2) hydrogen bonds : bond 0.07190 / 4.65 ( 940) hydrogen bonds : angle 5.12498 / 3.60 ( 2373) metal coordination : bond 0.00406 / 0.21 ( 3) Misc. bond : bond 0.01006 / 0.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 149 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8339 (m-80) cc_final: 0.7686 (m-80) REVERT: E 49 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8591 (ttm-80) REVERT: K 118 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: K 194 ASP cc_start: 0.7331 (p0) cc_final: 0.6922 (t70) REVERT: M 931 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8531 (tt) REVERT: N 44 VAL cc_start: 0.8583 (t) cc_final: 0.8364 (p) REVERT: N 64 MET cc_start: 0.8207 (ttt) cc_final: 0.7877 (tmm) REVERT: N 244 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: Q 67 LEU cc_start: 0.7802 (mp) cc_final: 0.7597 (mp) REVERT: L 254 LYS cc_start: 0.8366 (mptp) cc_final: 0.8102 (tptm) REVERT: L 264 TYR cc_start: 0.4333 (OUTLIER) cc_final: 0.3840 (m-10) REVERT: O 121 PHE cc_start: 0.8028 (t80) cc_final: 0.7209 (t80) REVERT: O 122 LEU cc_start: 0.7871 (mp) cc_final: 0.7576 (mp) REVERT: P 99 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6886 (pp) outliers start: 86 outliers final: 62 residues processed: 224 average time/residue: 0.1576 time to fit residues: 57.4650 Evaluate side-chains 203 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 136 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 244 GLN Chi-restraints excluded: chain N residue 352 ILE Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 264 TYR Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [121, 25, 45, 128, 98, 152, 183, 161, 242, 27, 5] chunk 121 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 ASN N 300 HIS ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.097511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067735 restraints weight = 93359.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068714 restraints weight = 54341.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068467 restraints weight = 35651.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068829 restraints weight = 34467.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068903 restraints weight = 30240.361| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25530 Z= 0.161 Angle : 0.674 11.269 35764 Z= 0.369 Chirality : 0.047 0.384 4040 Planarity : 0.004 0.057 3532 Dihedral : 27.051 175.107 5730 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 3.52 % Allowed : 20.24 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 2266 helix: -0.60 (0.18), residues: 730 sheet: -1.75 (0.26), residues: 351 loop : -1.93 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 74 TYR 0.017 0.001 TYR G 57 PHE 0.014 0.001 PHE L 293 TRP 0.010 0.001 TRP K 282 HIS 0.012 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (25525) covalent geometry : angle 0.67350 / 0.37 (35762) SS BOND : bond 0.01220 / 0.64 ( 1) SS BOND : angle 1.98619 / 1.11 ( 2) hydrogen bonds : bond 0.05959 / 3.84 ( 940) hydrogen bonds : angle 4.75289 / 3.35 ( 2373) metal coordination : bond 0.00702 / 0.35 ( 3) Misc. bond : bond 0.01096 / 0.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8283 (m-80) cc_final: 0.7599 (m-80) REVERT: E 49 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8590 (ttm-80) REVERT: H 39 TYR cc_start: 0.7541 (t80) cc_final: 0.7215 (t80) REVERT: K 118 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6165 (m-10) REVERT: K 130 MET cc_start: 0.6971 (mmt) cc_final: 0.6680 (mmt) REVERT: K 194 ASP cc_start: 0.7282 (p0) cc_final: 0.6902 (t70) REVERT: M 931 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8613 (tt) REVERT: M 959 TYR cc_start: 0.7898 (m-80) cc_final: 0.7134 (m-80) REVERT: N 44 VAL cc_start: 0.8545 (t) cc_final: 0.8313 (p) REVERT: N 244 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: Q 67 LEU cc_start: 0.7833 (mp) cc_final: 0.7601 (mp) REVERT: L 254 LYS cc_start: 0.8213 (mptp) cc_final: 0.8002 (tptm) REVERT: L 264 TYR cc_start: 0.4380 (OUTLIER) cc_final: 0.3882 (m-10) REVERT: O 121 PHE cc_start: 0.8015 (t80) cc_final: 0.7231 (t80) REVERT: O 122 LEU cc_start: 0.7878 (mp) cc_final: 0.7593 (mp) outliers start: 71 outliers final: 48 residues processed: 213 average time/residue: 0.1487 time to fit residues: 51.2056 Evaluate side-chains 195 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 244 GLN Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 264 TYR Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [64, 235, 102, 242, 192, 103, 107, 115, 142, 92, 54] chunk 64 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 47 GLN K 68 HIS M 852 GLN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 ASN ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.095733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.066009 restraints weight = 94638.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066521 restraints weight = 55711.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066150 restraints weight = 40547.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066518 restraints weight = 40796.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066790 restraints weight = 34302.892| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 25530 Z= 0.320 Angle : 0.796 9.780 35764 Z= 0.420 Chirality : 0.051 0.356 4040 Planarity : 0.005 0.061 3532 Dihedral : 27.226 171.971 5730 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 5.21 % Allowed : 20.09 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2266 helix: -0.75 (0.18), residues: 733 sheet: -1.72 (0.26), residues: 355 loop : -2.00 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 319 TYR 0.026 0.002 TYR G 57 PHE 0.019 0.002 PHE M 934 TRP 0.011 0.002 TRP K 197 HIS 0.009 0.002 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.32 (25525) covalent geometry : angle 0.79540 / 0.42 (35762) SS BOND : bond 0.02340 / 1.23 ( 1) SS BOND : angle 5.62398 / 2.96 ( 2) hydrogen bonds : bond 0.07132 / 4.60 ( 940) hydrogen bonds : angle 4.90402 / 3.44 ( 2373) metal coordination : bond 0.00356 / 0.18 ( 3) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 149 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.8918 (ttp-110) cc_final: 0.8667 (ttm-80) REVERT: G 77 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8066 (ptp-110) REVERT: K 37 SER cc_start: 0.7602 (OUTLIER) cc_final: 0.7160 (t) REVERT: K 105 ARG cc_start: 0.7641 (tmm160) cc_final: 0.7406 (tmm-80) REVERT: K 118 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6327 (m-10) REVERT: K 130 MET cc_start: 0.7102 (mmt) cc_final: 0.6820 (mmt) REVERT: K 194 ASP cc_start: 0.7352 (p0) cc_final: 0.6999 (t70) REVERT: M 831 GLN cc_start: 0.6910 (mp10) cc_final: 0.6396 (pp30) REVERT: M 852 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: M 931 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8604 (tt) REVERT: M 959 TYR cc_start: 0.7934 (m-80) cc_final: 0.7248 (m-80) REVERT: N 64 MET cc_start: 0.8328 (ttm) cc_final: 0.7793 (tmm) REVERT: N 214 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8166 (mt) REVERT: N 244 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: Q 67 LEU cc_start: 0.7914 (mp) cc_final: 0.7690 (mp) REVERT: R 6 THR cc_start: 0.6940 (OUTLIER) cc_final: 0.6727 (t) REVERT: X 320 THR cc_start: 0.5322 (OUTLIER) cc_final: 0.2984 (m) REVERT: L 264 TYR cc_start: 0.4668 (OUTLIER) cc_final: 0.3924 (m-10) REVERT: O 103 MET cc_start: 0.6900 (ttt) cc_final: 0.6333 (tpp) REVERT: O 121 PHE cc_start: 0.8045 (t80) cc_final: 0.7268 (t80) REVERT: O 122 LEU cc_start: 0.7771 (mp) cc_final: 0.7513 (mp) REVERT: P 103 MET cc_start: 0.2499 (OUTLIER) cc_final: 0.2015 (mmm) outliers start: 105 outliers final: 74 residues processed: 239 average time/residue: 0.1481 time to fit residues: 57.0828 Evaluate side-chains 226 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 141 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 852 GLN Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain M residue 971 THR Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 214 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 244 GLN Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 352 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 207 GLU Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 253 TYR Chi-restraints excluded: chain L residue 264 TYR Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 395 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 103 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [67, 100, 167, 11, 184, 29, 220, 235, 25, 232, 63] chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.0170 chunk 167 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K 186 HIS M 852 GLN N 278 ASN ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.097457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067125 restraints weight = 93591.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.068438 restraints weight = 51958.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068416 restraints weight = 37324.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068662 restraints weight = 30003.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068695 restraints weight = 29383.397| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25530 Z= 0.146 Angle : 0.656 9.500 35764 Z= 0.362 Chirality : 0.046 0.361 4040 Planarity : 0.004 0.062 3532 Dihedral : 26.954 172.239 5730 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.57 % Allowed : 22.57 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2266 helix: -0.21 (0.19), residues: 735 sheet: -1.37 (0.27), residues: 332 loop : -1.95 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 147 TYR 0.020 0.001 TYR G 57 PHE 0.017 0.001 PHE N 10 TRP 0.010 0.001 TRP K 282 HIS 0.009 0.001 HIS L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (25525) covalent geometry : angle 0.65614 / 0.36 (35762) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 1.80264 / 0.95 ( 2) hydrogen bonds : bond 0.05731 / 3.68 ( 940) hydrogen bonds : angle 4.53113 / 3.19 ( 2373) metal coordination : bond 0.00584 / 0.29 ( 3) Misc. bond : bond 0.02362 / 1.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 155 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.8922 (ttp-110) cc_final: 0.8689 (ttm-80) REVERT: H 39 TYR cc_start: 0.7541 (t80) cc_final: 0.7286 (t80) REVERT: K 37 SER cc_start: 0.7342 (OUTLIER) cc_final: 0.6899 (t) REVERT: K 118 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6272 (m-10) REVERT: K 130 MET cc_start: 0.7008 (mmt) cc_final: 0.6736 (mmt) REVERT: K 194 ASP cc_start: 0.7256 (p0) cc_final: 0.6858 (t70) REVERT: M 831 GLN cc_start: 0.6822 (mp10) cc_final: 0.6333 (pp30) REVERT: M 931 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8608 (tt) REVERT: M 959 TYR cc_start: 0.7872 (m-80) cc_final: 0.7148 (m-80) REVERT: N 64 MET cc_start: 0.8084 (ttm) cc_final: 0.7679 (tmm) REVERT: N 244 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: Q 67 LEU cc_start: 0.7628 (mp) cc_final: 0.7419 (mp) REVERT: R 6 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6639 (t) REVERT: X 203 ASP cc_start: 0.8731 (t0) cc_final: 0.8316 (m-30) REVERT: X 320 THR cc_start: 0.3133 (OUTLIER) cc_final: 0.2765 (p) REVERT: O 103 MET cc_start: 0.6866 (ttt) cc_final: 0.6413 (tpp) REVERT: O 121 PHE cc_start: 0.7969 (t80) cc_final: 0.7222 (t80) REVERT: O 122 LEU cc_start: 0.7746 (mp) cc_final: 0.7475 (mp) REVERT: P 103 MET cc_start: 0.2464 (OUTLIER) cc_final: 0.2042 (mmm) outliers start: 72 outliers final: 54 residues processed: 213 average time/residue: 0.1568 time to fit residues: 53.9250 Evaluate side-chains 209 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 244 GLN Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 207 GLU Chi-restraints excluded: chain X residue 320 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 103 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [169, 26, 157, 46, 10, 212, 90, 191, 149, 110, 236] chunk 169 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN M 920 ASN X 200 ASN L 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.097235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069912 restraints weight = 93240.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069047 restraints weight = 57141.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.069202 restraints weight = 45811.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.069449 restraints weight = 42415.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.069599 restraints weight = 35880.684| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25530 Z= 0.165 Angle : 0.654 9.575 35764 Z= 0.357 Chirality : 0.046 0.358 4040 Planarity : 0.004 0.065 3532 Dihedral : 26.855 170.897 5730 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 3.82 % Allowed : 22.62 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2266 helix: -0.01 (0.19), residues: 737 sheet: -1.35 (0.27), residues: 345 loop : -1.88 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.025 0.001 TYR G 57 PHE 0.016 0.001 PHE N 10 TRP 0.009 0.001 TRP N 348 HIS 0.009 0.001 HIS L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (25525) covalent geometry : angle 0.65443 / 0.36 (35762) SS BOND : bond 0.00926 / 0.49 ( 1) SS BOND : angle 1.23493 / 0.65 ( 2) hydrogen bonds : bond 0.05702 / 3.64 ( 940) hydrogen bonds : angle 4.43066 / 3.13 ( 2373) metal coordination : bond 0.00507 / 0.25 ( 3) Misc. bond : bond 0.00577 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 148 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: E 49 ARG cc_start: 0.8883 (ttp-110) cc_final: 0.8662 (ttm-80) REVERT: H 39 TYR cc_start: 0.7543 (t80) cc_final: 0.7245 (t80) REVERT: K 37 SER cc_start: 0.7192 (OUTLIER) cc_final: 0.6753 (t) REVERT: K 130 MET cc_start: 0.7029 (mmt) cc_final: 0.6735 (mmt) REVERT: K 194 ASP cc_start: 0.7204 (p0) cc_final: 0.6875 (t70) REVERT: M 831 GLN cc_start: 0.6804 (mp10) cc_final: 0.6311 (pp30) REVERT: M 931 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8753 (tt) REVERT: M 959 TYR cc_start: 0.7926 (m-80) cc_final: 0.7223 (m-80) REVERT: N 64 MET cc_start: 0.8008 (ttm) cc_final: 0.7679 (tmm) REVERT: N 214 ILE cc_start: 0.8258 (pt) cc_final: 0.7957 (mm) REVERT: N 244 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: Q 67 LEU cc_start: 0.7725 (mp) cc_final: 0.7511 (mp) REVERT: X 203 ASP cc_start: 0.8528 (t0) cc_final: 0.8145 (m-30) REVERT: O 103 MET cc_start: 0.6707 (ttt) cc_final: 0.6103 (tpp) REVERT: O 121 PHE cc_start: 0.7841 (t80) cc_final: 0.7118 (t80) REVERT: P 103 MET cc_start: 0.2582 (OUTLIER) cc_final: 0.2005 (mmm) outliers start: 77 outliers final: 60 residues processed: 212 average time/residue: 0.1559 time to fit residues: 54.0255 Evaluate side-chains 209 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 244 GLN Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 352 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 207 GLU Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 253 TYR Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 103 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [51, 176, 111, 195, 69, 42, 73, 153, 104, 121, 186] chunk 51 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 153 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN R 5 GLN L 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.098288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068245 restraints weight = 93484.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069427 restraints weight = 51257.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070220 restraints weight = 34572.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070107 restraints weight = 29814.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070078 restraints weight = 26578.115| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25530 Z= 0.128 Angle : 0.628 9.646 35764 Z= 0.346 Chirality : 0.045 0.360 4040 Planarity : 0.004 0.066 3532 Dihedral : 26.621 169.629 5730 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.37 % Allowed : 22.77 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2266 helix: 0.27 (0.19), residues: 736 sheet: -1.25 (0.26), residues: 350 loop : -1.80 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 89 TYR 0.023 0.001 TYR G 57 PHE 0.021 0.001 PHE O 121 TRP 0.009 0.001 TRP K 282 HIS 0.012 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (25525) covalent geometry : angle 0.62801 / 0.35 (35762) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 1.29860 / 0.71 ( 2) hydrogen bonds : bond 0.05460 / 3.45 ( 940) hydrogen bonds : angle 4.26932 / 3.02 ( 2373) metal coordination : bond 0.00621 / 0.31 ( 3) Misc. bond : bond 0.00305 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7523 (mt-10) REVERT: D 56 MET cc_start: 0.8713 (tpp) cc_final: 0.8452 (tpp) REVERT: E 41 TYR cc_start: 0.8251 (m-80) cc_final: 0.7683 (m-80) REVERT: E 49 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8656 (ttm-80) REVERT: H 39 TYR cc_start: 0.7503 (t80) cc_final: 0.7252 (t80) REVERT: K 37 SER cc_start: 0.7131 (OUTLIER) cc_final: 0.6671 (t) REVERT: K 194 ASP cc_start: 0.7167 (p0) cc_final: 0.6837 (t70) REVERT: M 831 GLN cc_start: 0.6783 (mp10) cc_final: 0.6348 (pp30) REVERT: M 931 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (tt) REVERT: M 959 TYR cc_start: 0.7907 (m-80) cc_final: 0.7208 (m-80) REVERT: N 64 MET cc_start: 0.8012 (ttm) cc_final: 0.7550 (tmm) REVERT: N 214 ILE cc_start: 0.8218 (pt) cc_final: 0.7929 (mm) REVERT: Q 67 LEU cc_start: 0.7558 (mp) cc_final: 0.7336 (mp) REVERT: X 203 ASP cc_start: 0.8690 (t0) cc_final: 0.8290 (m-30) REVERT: L 62 MET cc_start: 0.4721 (mmt) cc_final: 0.2915 (pmm) REVERT: L 82 MET cc_start: 0.5580 (mmp) cc_final: 0.4759 (mmp) REVERT: O 103 MET cc_start: 0.6976 (ttt) cc_final: 0.6311 (tpp) REVERT: O 121 PHE cc_start: 0.8007 (t80) cc_final: 0.7240 (t80) REVERT: O 122 LEU cc_start: 0.7486 (mp) cc_final: 0.7276 (mp) REVERT: P 103 MET cc_start: 0.2730 (OUTLIER) cc_final: 0.2255 (mmm) outliers start: 68 outliers final: 56 residues processed: 212 average time/residue: 0.1589 time to fit residues: 54.5783 Evaluate side-chains 204 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 145 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 207 GLU Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 103 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [166, 196, 122, 103, 82, 211, 26, 18, 192, 134, 169] chunk 166 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS P 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.096572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066192 restraints weight = 95192.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067614 restraints weight = 54138.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.067174 restraints weight = 36045.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067592 restraints weight = 38580.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067460 restraints weight = 33209.323| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25530 Z= 0.239 Angle : 0.697 9.204 35764 Z= 0.374 Chirality : 0.047 0.347 4040 Planarity : 0.005 0.066 3532 Dihedral : 26.806 167.496 5728 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 3.42 % Allowed : 22.97 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.17), residues: 2266 helix: 0.06 (0.19), residues: 739 sheet: -1.33 (0.26), residues: 355 loop : -1.86 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 116 TYR 0.023 0.002 TYR G 57 PHE 0.033 0.002 PHE P 121 TRP 0.011 0.001 TRP N 95 HIS 0.009 0.001 HIS L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (25525) covalent geometry : angle 0.69747 / 0.37 (35762) SS BOND : bond 0.00595 / 0.31 ( 1) SS BOND : angle 0.66268 / 0.36 ( 2) hydrogen bonds : bond 0.06072 / 3.88 ( 940) hydrogen bonds : angle 4.41168 / 3.11 ( 2373) metal coordination : bond 0.00503 / 0.25 ( 3) Misc. bond : bond 0.00188 / 0.10 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 142 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.8837 (tpp) cc_final: 0.8547 (tpp) REVERT: E 41 TYR cc_start: 0.7983 (m-80) cc_final: 0.7693 (m-80) REVERT: E 49 ARG cc_start: 0.8875 (ttp-110) cc_final: 0.8636 (ttm-80) REVERT: H 39 TYR cc_start: 0.7570 (t80) cc_final: 0.7271 (t80) REVERT: K 37 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.6896 (t) REVERT: K 194 ASP cc_start: 0.7306 (p0) cc_final: 0.6889 (t70) REVERT: M 831 GLN cc_start: 0.7001 (mp10) cc_final: 0.6450 (pp30) REVERT: M 931 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (tt) REVERT: M 959 TYR cc_start: 0.7902 (m-80) cc_final: 0.7231 (m-80) REVERT: N 64 MET cc_start: 0.8135 (ttm) cc_final: 0.7617 (tmm) REVERT: N 214 ILE cc_start: 0.8316 (pt) cc_final: 0.8058 (mm) REVERT: X 203 ASP cc_start: 0.8684 (t0) cc_final: 0.8276 (m-30) REVERT: L 62 MET cc_start: 0.4713 (mmt) cc_final: 0.2910 (pmm) REVERT: L 86 ASP cc_start: 0.4930 (OUTLIER) cc_final: 0.4520 (t70) REVERT: O 103 MET cc_start: 0.7118 (ttt) cc_final: 0.6279 (tpp) REVERT: P 103 MET cc_start: 0.2768 (OUTLIER) cc_final: 0.2304 (mmm) outliers start: 69 outliers final: 62 residues processed: 200 average time/residue: 0.1530 time to fit residues: 49.8770 Evaluate side-chains 206 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 118 TYR Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 279 MET Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 825 VAL Chi-restraints excluded: chain M residue 878 ILE Chi-restraints excluded: chain M residue 888 VAL Chi-restraints excluded: chain M residue 931 ILE Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 181 ILE Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain X residue 205 VAL Chi-restraints excluded: chain X residue 207 GLU Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 395 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 92 ASN Chi-restraints excluded: chain P residue 103 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [25, 124, 203, 147, 19, 40, 182, 131, 37, 107, 66] chunk 25 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.098081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068306 restraints weight = 93782.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069791 restraints weight = 55182.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.069298 restraints weight = 34665.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069740 restraints weight = 36183.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069702 restraints weight = 31150.159| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25530 Z= 0.136 Angle : 0.630 12.086 35764 Z= 0.346 Chirality : 0.045 0.355 4040 Planarity : 0.004 0.064 3532 Dihedral : 26.588 166.608 5728 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 3.32 % Allowed : 23.21 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2266 helix: 0.35 (0.19), residues: 736 sheet: -1.16 (0.27), residues: 342 loop : -1.74 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 903 TYR 0.026 0.001 TYR G 57 PHE 0.020 0.001 PHE O 121 TRP 0.010 0.001 TRP N 348 HIS 0.010 0.001 HIS L 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (25525) covalent geometry : angle 0.63010 / 0.35 (35762) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 0.64859 / 0.36 ( 2) hydrogen bonds : bond 0.05433 / 3.43 ( 940) hydrogen bonds : angle 4.23227 / 3.00 ( 2373) metal coordination : bond 0.00694 / 0.35 ( 3) Misc. bond : bond 0.00976 / 0.51 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.93 seconds wall clock time: 80 minutes 43.66 seconds (4843.66 seconds total)