Starting phenix.real_space_refine on Thu Mar 5 17:57:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uh5_20767/03_2026/6uh5_20767.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uh5_20767/03_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_20767/03_2026/6uh5_20767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uh5_20767/03_2026/6uh5_20767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uh5_20767/03_2026/6uh5_20767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uh5_20767/03_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-dev-5986/lib/python3.9/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: 5.01, per 1000 atoms: 0.20 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: 1.61 Conformation dependent library (CDL) restraints added in 903.3 milliseconds 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: 3.18 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: 5.16 Time building geometry restraints manager: 2.26 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=" 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=" N PRO N 9 " pdb=" CD PRO N 9 " ideal model delta sigma weight residual 1.474 1.531 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C SER X 221 " pdb=" N PRO X 222 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" CA PRO Q 37 " pdb=" C PRO Q 37 " ideal model delta sigma weight residual 1.517 1.496 0.021 6.70e-03 2.23e+04 9.86e+00 bond pdb=" C GLN M 894 " pdb=" N PRO M 895 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.30e-02 5.92e+03 8.42e+00 ... (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: 12941 35.43 - 70.87: 1637 70.87 - 106.30: 40 106.30 - 141.74: 1 141.74 - 177.17: 2 Dihedral angle restraints: 14621 sinusoidal: 7864 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 14618 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.720 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.617 25530 Z= 0.528 Angle : 1.396 37.118 35764 Z= 0.845 Chirality : 0.090 1.543 4040 Planarity : 0.007 0.087 3532 Dihedral : 23.785 177.172 10248 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 covalent geometry : bond 0.01116 (25525) covalent geometry : angle 1.39598 (35762) SS BOND : bond 0.01138 ( 1) SS BOND : angle 2.44313 ( 2) hydrogen bonds : bond 0.30076 ( 940) hydrogen bonds : angle 10.51608 ( 2373) metal coordination : bond 0.50052 ( 3) Misc. bond : bond 0.00517 ( 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 : 0.798 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 41 TYR cc_start: 0.8409 (m-80) cc_final: 0.8033 (m-80) REVERT: E 49 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8231 (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: 0.5930 (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: 0.6458 (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: 0.6784 (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: 0.8011 (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: 0.6685 (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: 0.6799 (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: 0.1960 time to fit residues: 88.2894 Evaluate side-chains 173 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 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: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN 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 M 743 ASN M 827 GLN M 852 GLN N 149 ASN N 175 HIS ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 412 ASN Q 68 HIS X 322 GLN L 55 GLN L 133 HIS L 172 HIS L 255 ASN L 317 GLN L 325 HIS L 344 ASN ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.098443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067633 restraints weight = 94943.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069338 restraints weight = 53834.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068259 restraints weight = 36708.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068705 restraints weight = 38988.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.068746 restraints weight = 32705.042| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25530 Z= 0.255 Angle : 0.734 9.265 35764 Z= 0.410 Chirality : 0.045 0.194 4040 Planarity : 0.006 0.067 3532 Dihedral : 27.158 177.971 5774 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 3.17 % Allowed : 15.13 % Favored : 81.70 % 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: -3.38 (0.15), residues: 2266 helix: -2.03 (0.16), residues: 752 sheet: -2.21 (0.24), residues: 359 loop : -2.37 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 298 TYR 0.024 0.002 TYR M 972 PHE 0.020 0.002 PHE O 121 TRP 0.014 0.002 TRP K 137 HIS 0.014 0.002 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00571 (25525) covalent geometry : angle 0.73353 (35762) SS BOND : bond 0.02033 ( 1) SS BOND : angle 2.53047 ( 2) hydrogen bonds : bond 0.06583 ( 940) hydrogen bonds : angle 5.53271 ( 2373) metal coordination : bond 0.00780 ( 3) Misc. bond : bond 0.00301 ( 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 248 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8374 (m-80) cc_final: 0.8097 (m-80) REVERT: E 49 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8378 (ttm-80) REVERT: E 59 GLU cc_start: 0.7822 (pm20) cc_final: 0.7576 (pm20) REVERT: H 105 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7934 (ttpp) REVERT: K 51 MET cc_start: 0.8389 (mmm) cc_final: 0.8148 (ptm) REVERT: K 118 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: K 194 ASP cc_start: 0.7273 (p0) cc_final: 0.6954 (t70) REVERT: K 234 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7830 (mmm160) REVERT: M 931 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8623 (tt) REVERT: N 24 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8622 (mp) REVERT: N 64 MET cc_start: 0.7928 (ttt) cc_final: 0.7631 (tmm) REVERT: L 62 MET cc_start: 0.6083 (mpp) cc_final: 0.5817 (mmt) REVERT: L 144 SER cc_start: 0.7405 (m) cc_final: 0.7095 (p) REVERT: O 103 MET cc_start: 0.5962 (tpt) cc_final: 0.5472 (tpt) REVERT: O 121 PHE cc_start: 0.7753 (t80) cc_final: 0.7107 (t80) REVERT: O 122 LEU cc_start: 0.7809 (mp) cc_final: 0.7559 (mp) outliers start: 64 outliers final: 31 residues processed: 239 average time/residue: 0.1669 time to fit residues: 62.0351 Evaluate side-chains 186 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 34 TYR 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 24 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 7 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain X residue 323 LEU Chi-restraints excluded: chain L residue 86 ASP 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 123 ILE 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: chunk 247 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 73 ASN H 46 HIS K 47 GLN K 68 HIS K 138 HIS ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 300 HIS Q 25 ASN X 200 ASN L 228 ASN L 325 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.097079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066910 restraints weight = 94369.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067989 restraints weight = 51755.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067745 restraints weight = 33669.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067981 restraints weight = 34739.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067932 restraints weight = 33061.672| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 25530 Z= 0.253 Angle : 0.683 9.107 35764 Z= 0.381 Chirality : 0.043 0.198 4040 Planarity : 0.005 0.062 3532 Dihedral : 26.838 173.607 5761 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.70 % Rotamer: Outliers : 3.57 % Allowed : 17.51 % Favored : 78.92 % 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: -2.62 (0.16), residues: 2266 helix: -1.16 (0.18), residues: 734 sheet: -1.91 (0.26), residues: 339 loop : -2.06 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 104 TYR 0.019 0.002 TYR G 57 PHE 0.018 0.002 PHE X 327 TRP 0.010 0.001 TRP K 137 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00572 (25525) covalent geometry : angle 0.68325 (35762) SS BOND : bond 0.03250 ( 1) SS BOND : angle 1.57752 ( 2) hydrogen bonds : bond 0.06209 ( 940) hydrogen bonds : angle 4.98901 ( 2373) metal coordination : bond 0.00909 ( 3) Misc. bond : bond 0.00186 ( 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 247 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8547 (tp-100) REVERT: E 41 TYR cc_start: 0.8372 (m-80) cc_final: 0.7837 (m-80) REVERT: E 49 ARG cc_start: 0.8865 (ttp-110) cc_final: 0.8610 (ttm-80) REVERT: H 105 LYS cc_start: 0.8427 (ttpt) cc_final: 0.7964 (ttpp) REVERT: K 118 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6229 (m-10) REVERT: K 194 ASP cc_start: 0.7368 (p0) cc_final: 0.6970 (t70) REVERT: M 924 ASP cc_start: 0.7801 (t0) cc_final: 0.7566 (t0) REVERT: M 931 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8563 (tt) REVERT: M 959 TYR cc_start: 0.7980 (m-80) cc_final: 0.7178 (m-80) REVERT: N 64 MET cc_start: 0.8015 (ttt) cc_final: 0.7634 (tmm) REVERT: N 364 GLU cc_start: 0.7808 (tp30) cc_final: 0.7542 (mm-30) REVERT: L 144 SER cc_start: 0.7557 (m) cc_final: 0.7233 (p) REVERT: L 254 LYS cc_start: 0.8145 (mptp) cc_final: 0.7840 (tptm) REVERT: O 121 PHE cc_start: 0.7915 (t80) cc_final: 0.7192 (t80) REVERT: O 122 LEU cc_start: 0.7889 (mp) cc_final: 0.7605 (mp) outliers start: 72 outliers final: 44 residues processed: 234 average time/residue: 0.1610 time to fit residues: 60.0812 Evaluate side-chains 199 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS 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 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 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 34 TYR 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 129 SER Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 243 TRP 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 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 140 TYR Chi-restraints excluded: chain N residue 143 THR 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 403 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 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER 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: chunk 244 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 174 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN K 186 HIS N 278 ASN Q 25 ASN ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.098173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068150 restraints weight = 93609.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.069121 restraints weight = 53654.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069460 restraints weight = 38456.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069832 restraints weight = 30832.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069663 restraints weight = 28599.413| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25530 Z= 0.181 Angle : 0.628 10.442 35764 Z= 0.350 Chirality : 0.041 0.208 4040 Planarity : 0.004 0.063 3532 Dihedral : 26.525 174.537 5760 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 3.87 % Allowed : 18.85 % Favored : 77.28 % 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: -2.13 (0.17), residues: 2266 helix: -0.49 (0.19), residues: 734 sheet: -1.73 (0.26), residues: 348 loop : -1.92 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 234 TYR 0.030 0.001 TYR H 80 PHE 0.015 0.001 PHE L 293 TRP 0.008 0.001 TRP K 137 HIS 0.008 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00406 (25525) covalent geometry : angle 0.62767 (35762) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.32144 ( 2) hydrogen bonds : bond 0.05264 ( 940) hydrogen bonds : angle 4.58207 ( 2373) metal coordination : bond 0.00614 ( 3) Misc. bond : bond 0.00203 ( 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 253 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8603 (tp-100) REVERT: E 41 TYR cc_start: 0.8397 (m-80) cc_final: 0.7889 (m-80) REVERT: E 49 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8630 (ttm-80) REVERT: E 50 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8025 (mm-30) REVERT: H 39 TYR cc_start: 0.7533 (t80) cc_final: 0.7189 (t80) REVERT: K 37 SER cc_start: 0.7335 (OUTLIER) cc_final: 0.6989 (t) REVERT: K 51 MET cc_start: 0.8534 (mmm) cc_final: 0.8331 (ttt) REVERT: K 118 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: K 194 ASP cc_start: 0.7338 (p0) cc_final: 0.6973 (t70) REVERT: M 931 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8570 (tt) REVERT: M 959 TYR cc_start: 0.7921 (m-80) cc_final: 0.7224 (m-80) REVERT: N 64 MET cc_start: 0.8028 (ttt) cc_final: 0.7656 (tmm) REVERT: N 214 ILE cc_start: 0.8144 (pt) cc_final: 0.7807 (mm) REVERT: N 364 GLU cc_start: 0.7759 (tp30) cc_final: 0.7453 (mm-30) REVERT: Q 67 LEU cc_start: 0.7528 (mp) cc_final: 0.7315 (mp) REVERT: X 203 ASP cc_start: 0.8445 (t0) cc_final: 0.8033 (m-30) REVERT: L 62 MET cc_start: 0.5011 (mmt) cc_final: 0.4653 (mmt) REVERT: O 103 MET cc_start: 0.6270 (tpt) cc_final: 0.5669 (tpp) REVERT: O 121 PHE cc_start: 0.7987 (t80) cc_final: 0.7302 (t80) REVERT: O 122 LEU cc_start: 0.7892 (mp) cc_final: 0.7560 (mp) REVERT: P 88 ARG cc_start: 0.6754 (tpp-160) cc_final: 0.6220 (ttp-110) outliers start: 78 outliers final: 49 residues processed: 240 average time/residue: 0.1478 time to fit residues: 57.1676 Evaluate side-chains 206 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 21 VAL 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 118 TYR 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 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 124 VAL 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 N residue 280 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 44 ILE 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 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER 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 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 128 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN R 5 GLN L 325 HIS P 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.099084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.069404 restraints weight = 93628.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070633 restraints weight = 52447.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.070960 restraints weight = 35434.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071188 restraints weight = 30263.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071061 restraints weight = 28369.662| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25530 Z= 0.138 Angle : 0.591 8.839 35764 Z= 0.332 Chirality : 0.040 0.189 4040 Planarity : 0.004 0.055 3532 Dihedral : 26.238 174.447 5758 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 3.52 % Allowed : 20.19 % Favored : 76.29 % 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: -1.74 (0.17), residues: 2266 helix: -0.04 (0.19), residues: 740 sheet: -1.44 (0.27), residues: 352 loop : -1.81 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 325 TYR 0.015 0.001 TYR G 57 PHE 0.014 0.001 PHE L 293 TRP 0.007 0.001 TRP K 282 HIS 0.008 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00302 (25525) covalent geometry : angle 0.59120 (35762) SS BOND : bond 0.00493 ( 1) SS BOND : angle 1.31439 ( 2) hydrogen bonds : bond 0.05026 ( 940) hydrogen bonds : angle 4.31286 ( 2373) metal coordination : bond 0.00672 ( 3) Misc. bond : bond 0.00475 ( 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 242 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 171 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8589 (tp-100) REVERT: E 41 TYR cc_start: 0.8348 (m-80) cc_final: 0.7749 (m-80) REVERT: E 49 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8644 (ttm-80) REVERT: H 39 TYR cc_start: 0.7407 (t80) cc_final: 0.7053 (t80) REVERT: K 37 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6797 (t) REVERT: K 194 ASP cc_start: 0.7357 (p0) cc_final: 0.7025 (t70) REVERT: M 931 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8549 (tt) REVERT: M 959 TYR cc_start: 0.7947 (m-80) cc_final: 0.7256 (m-80) REVERT: N 214 ILE cc_start: 0.8180 (pt) cc_final: 0.7872 (mm) REVERT: N 364 GLU cc_start: 0.7838 (tp30) cc_final: 0.7601 (mm-30) REVERT: Q 1 MET cc_start: 0.5525 (tmm) cc_final: 0.5286 (tmm) REVERT: Q 67 LEU cc_start: 0.7447 (mp) cc_final: 0.7184 (mp) REVERT: X 203 ASP cc_start: 0.8482 (t0) cc_final: 0.8038 (m-30) REVERT: L 86 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4477 (t70) REVERT: L 259 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.5870 (t80) REVERT: O 103 MET cc_start: 0.6394 (tpt) cc_final: 0.5681 (tpp) REVERT: O 121 PHE cc_start: 0.7964 (t80) cc_final: 0.7248 (t80) REVERT: O 122 LEU cc_start: 0.7933 (mp) cc_final: 0.7713 (mp) outliers start: 71 outliers final: 43 residues processed: 227 average time/residue: 0.1488 time to fit residues: 54.2751 Evaluate side-chains 200 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS 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 92 GLU Chi-restraints excluded: chain C residue 113 SER 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 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 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 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 143 THR Chi-restraints excluded: chain N residue 231 ILE Chi-restraints excluded: chain N residue 238 ARG Chi-restraints excluded: chain N residue 403 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 41 GLN 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 238 SER Chi-restraints excluded: chain L residue 259 TYR Chi-restraints excluded: chain L residue 297 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 64 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN M 852 GLN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 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 = 0.4041 r_free = 0.4041 target = 0.096407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067207 restraints weight = 94203.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067610 restraints weight = 56857.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066999 restraints weight = 42373.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067312 restraints weight = 43766.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067492 restraints weight = 36748.858| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 25530 Z= 0.309 Angle : 0.690 9.593 35764 Z= 0.380 Chirality : 0.044 0.198 4040 Planarity : 0.005 0.061 3532 Dihedral : 26.532 170.673 5757 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 4.27 % Allowed : 21.18 % Favored : 74.55 % 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: -1.85 (0.17), residues: 2266 helix: -0.26 (0.19), residues: 739 sheet: -1.39 (0.28), residues: 344 loop : -1.82 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 234 TYR 0.023 0.002 TYR H 80 PHE 0.013 0.002 PHE O 121 TRP 0.011 0.001 TRP N 95 HIS 0.008 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00702 (25525) covalent geometry : angle 0.69013 (35762) SS BOND : bond 0.00451 ( 1) SS BOND : angle 1.35763 ( 2) hydrogen bonds : bond 0.05963 ( 940) hydrogen bonds : angle 4.54475 ( 2373) metal coordination : bond 0.00537 ( 3) Misc. bond : bond 0.00351 ( 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 243 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 157 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8247 (m-80) cc_final: 0.7801 (m-80) REVERT: K 37 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7033 (t) REVERT: K 194 ASP cc_start: 0.7443 (p0) cc_final: 0.7182 (t70) REVERT: K 234 ARG cc_start: 0.8246 (mmm160) cc_final: 0.8026 (mmm160) REVERT: M 831 GLN cc_start: 0.7049 (mp10) cc_final: 0.6448 (pp30) REVERT: M 931 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8651 (tt) REVERT: M 959 TYR cc_start: 0.7900 (m-80) cc_final: 0.7249 (m-80) REVERT: N 364 GLU cc_start: 0.7863 (tp30) cc_final: 0.7506 (mm-30) REVERT: Q 67 LEU cc_start: 0.7571 (mp) cc_final: 0.7325 (mp) REVERT: X 203 ASP cc_start: 0.8490 (t0) cc_final: 0.8118 (m-30) REVERT: L 86 ASP cc_start: 0.4961 (OUTLIER) cc_final: 0.4577 (t70) REVERT: L 259 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5951 (t80) REVERT: O 103 MET cc_start: 0.6427 (tpt) cc_final: 0.5637 (tpp) REVERT: P 103 MET cc_start: 0.2588 (OUTLIER) cc_final: 0.2105 (mmm) outliers start: 86 outliers final: 62 residues processed: 225 average time/residue: 0.1509 time to fit residues: 54.3969 Evaluate side-chains 210 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 143 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 120 MET 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 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 101 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 56 GLU 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 53 VAL Chi-restraints excluded: chain K residue 68 HIS 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 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 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 N residue 403 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 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 238 SER Chi-restraints excluded: chain L residue 253 TYR Chi-restraints excluded: chain L residue 259 TYR Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 364 ILE 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 103 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.0770 chunk 167 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS L 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.098869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069193 restraints weight = 93619.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070541 restraints weight = 54574.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070469 restraints weight = 32904.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070856 restraints weight = 35041.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070730 restraints weight = 31565.775| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25530 Z= 0.135 Angle : 0.595 9.511 35764 Z= 0.332 Chirality : 0.040 0.186 4040 Planarity : 0.004 0.064 3532 Dihedral : 26.189 169.805 5757 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.93 % Allowed : 22.37 % 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: -1.40 (0.17), residues: 2266 helix: 0.30 (0.19), residues: 737 sheet: -1.20 (0.28), residues: 348 loop : -1.66 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 234 TYR 0.019 0.001 TYR G 57 PHE 0.017 0.001 PHE O 121 TRP 0.009 0.001 TRP K 282 HIS 0.009 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00296 (25525) covalent geometry : angle 0.59464 (35762) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.74689 ( 2) hydrogen bonds : bond 0.05039 ( 940) hydrogen bonds : angle 4.18272 ( 2373) metal coordination : bond 0.00594 ( 3) Misc. bond : bond 0.00123 ( 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 236 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8498 (tp-100) REVERT: H 39 TYR cc_start: 0.7460 (t80) cc_final: 0.7173 (t80) REVERT: H 44 GLN cc_start: 0.8406 (mt0) cc_final: 0.8127 (tt0) REVERT: K 37 SER cc_start: 0.6936 (OUTLIER) cc_final: 0.6450 (t) REVERT: K 194 ASP cc_start: 0.7324 (p0) cc_final: 0.7019 (t70) REVERT: K 254 TYR cc_start: 0.6731 (m-80) cc_final: 0.5575 (m-10) REVERT: M 959 TYR cc_start: 0.7919 (m-80) cc_final: 0.7240 (m-80) REVERT: N 56 MET cc_start: 0.7838 (mmm) cc_final: 0.7219 (mmm) REVERT: Q 67 LEU cc_start: 0.7367 (mp) cc_final: 0.7129 (mp) REVERT: X 203 ASP cc_start: 0.8747 (t0) cc_final: 0.8372 (m-30) REVERT: L 82 MET cc_start: 0.5936 (mmp) cc_final: 0.5148 (mmp) REVERT: L 86 ASP cc_start: 0.4958 (OUTLIER) cc_final: 0.4666 (t0) REVERT: L 259 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.5925 (t80) REVERT: O 103 MET cc_start: 0.6482 (tpt) cc_final: 0.6252 (ttt) REVERT: P 89 ARG cc_start: 0.6268 (mpt-90) cc_final: 0.6053 (mpt-90) outliers start: 59 outliers final: 42 residues processed: 225 average time/residue: 0.1515 time to fit residues: 54.5366 Evaluate side-chains 199 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 92 GLU 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 92 GLU 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 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 312 VAL Chi-restraints excluded: chain M residue 888 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 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 403 THR 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 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 259 TYR Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 395 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 169 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN M 831 GLN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS L 325 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.097065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067110 restraints weight = 93507.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067863 restraints weight = 54253.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068067 restraints weight = 40915.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068582 restraints weight = 32426.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.068524 restraints weight = 29543.384| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- 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 = 0.10 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 = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25530 Z= 0.213 Angle : 0.631 12.842 35764 Z= 0.348 Chirality : 0.042 0.199 4040 Planarity : 0.004 0.065 3532 Dihedral : 26.247 166.022 5757 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 3.12 % Allowed : 22.42 % Favored : 74.45 % 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: -1.46 (0.17), residues: 2266 helix: 0.20 (0.19), residues: 751 sheet: -1.21 (0.28), residues: 348 loop : -1.69 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 116 TYR 0.016 0.001 TYR G 57 PHE 0.025 0.002 PHE P 121 TRP 0.010 0.001 TRP N 95 HIS 0.009 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00484 (25525) covalent geometry : angle 0.63110 (35762) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.12690 ( 2) hydrogen bonds : bond 0.05415 ( 940) hydrogen bonds : angle 4.27711 ( 2373) metal coordination : bond 0.00555 ( 3) Misc. bond : bond 0.00087 ( 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 221 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8561 (tp-100) REVERT: D 56 MET cc_start: 0.8811 (tpp) cc_final: 0.8521 (tpp) REVERT: F 27 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8326 (mm-40) REVERT: K 37 SER cc_start: 0.7235 (OUTLIER) cc_final: 0.6705 (t) REVERT: K 194 ASP cc_start: 0.7449 (p0) cc_final: 0.7205 (t70) REVERT: K 254 TYR cc_start: 0.6836 (m-80) cc_final: 0.5624 (m-10) REVERT: M 831 GLN cc_start: 0.7286 (mp-120) cc_final: 0.6482 (pp30) REVERT: M 959 TYR cc_start: 0.7916 (m-80) cc_final: 0.7293 (m-80) REVERT: Q 67 LEU cc_start: 0.7608 (mp) cc_final: 0.7343 (mp) REVERT: X 203 ASP cc_start: 0.8688 (t0) cc_final: 0.8322 (m-30) REVERT: L 86 ASP cc_start: 0.4902 (OUTLIER) cc_final: 0.4610 (t0) REVERT: L 259 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5859 (t80) REVERT: O 103 MET cc_start: 0.6560 (tpt) cc_final: 0.5787 (tpp) outliers start: 63 outliers final: 50 residues processed: 209 average time/residue: 0.1443 time to fit residues: 48.8809 Evaluate side-chains 204 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 92 GLU Chi-restraints excluded: chain C residue 113 SER 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 56 GLU 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 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 825 VAL Chi-restraints excluded: chain M residue 888 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 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 N residue 403 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 66 THR 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 238 SER Chi-restraints excluded: chain L residue 259 TYR 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 89 ARG Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 51 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** N 266 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 = 0.4084 r_free = 0.4084 target = 0.098775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.069168 restraints weight = 94236.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.070672 restraints weight = 54962.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070217 restraints weight = 33896.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070666 restraints weight = 36181.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070667 restraints weight = 30622.770| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25530 Z= 0.136 Angle : 0.599 12.078 35764 Z= 0.332 Chirality : 0.040 0.186 4040 Planarity : 0.004 0.065 3532 Dihedral : 26.014 164.074 5757 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 2.63 % Allowed : 23.31 % Favored : 74.06 % 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: -1.18 (0.17), residues: 2266 helix: 0.56 (0.20), residues: 746 sheet: -1.07 (0.28), residues: 333 loop : -1.60 (0.17), residues: 1187 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 0.019 0.001 PHE P 121 TRP 0.009 0.001 TRP K 282 HIS 0.011 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00297 (25525) covalent geometry : angle 0.59934 (35762) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.67052 ( 2) hydrogen bonds : bond 0.04942 ( 940) hydrogen bonds : angle 4.10580 ( 2373) metal coordination : bond 0.00613 ( 3) Misc. bond : bond 0.00341 ( 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 227 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.619 Fit side-chains REVERT: C 84 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8516 (tp-100) REVERT: F 27 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8213 (mm-40) REVERT: H 44 GLN cc_start: 0.8419 (mt0) cc_final: 0.8159 (tt0) REVERT: K 37 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6455 (t) REVERT: K 194 ASP cc_start: 0.7347 (p0) cc_final: 0.6996 (t70) REVERT: K 254 TYR cc_start: 0.6960 (m-80) cc_final: 0.5805 (m-10) REVERT: M 873 TYR cc_start: 0.8295 (m-80) cc_final: 0.7898 (m-80) REVERT: M 939 CYS cc_start: 0.7471 (m) cc_final: 0.7154 (t) REVERT: M 959 TYR cc_start: 0.7980 (m-80) cc_final: 0.7278 (m-80) REVERT: N 56 MET cc_start: 0.7828 (mmm) cc_final: 0.7140 (mmm) REVERT: Q 67 LEU cc_start: 0.7540 (mp) cc_final: 0.7235 (mp) REVERT: X 203 ASP cc_start: 0.8833 (t0) cc_final: 0.8491 (m-30) REVERT: L 86 ASP cc_start: 0.5041 (OUTLIER) cc_final: 0.4795 (t0) REVERT: L 259 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.5901 (t80) REVERT: O 103 MET cc_start: 0.6985 (tpt) cc_final: 0.6255 (tpp) REVERT: O 121 PHE cc_start: 0.7971 (t80) cc_final: 0.7355 (t80) outliers start: 53 outliers final: 45 residues processed: 215 average time/residue: 0.1474 time to fit residues: 51.1857 Evaluate side-chains 204 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 92 GLU Chi-restraints excluded: chain C residue 113 SER 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 56 GLU Chi-restraints excluded: chain G residue 92 GLU 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 118 TYR Chi-restraints excluded: chain K residue 126 CYS 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 888 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 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 N residue 403 THR Chi-restraints excluded: chain Q residue 9 THR 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 259 TYR Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 395 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain O residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 166 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.097576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067736 restraints weight = 94299.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068413 restraints weight = 55070.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069804 restraints weight = 38269.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069830 restraints weight = 29352.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069616 restraints weight = 26256.526| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25530 Z= 0.194 Angle : 0.630 12.331 35764 Z= 0.346 Chirality : 0.041 0.190 4040 Planarity : 0.004 0.074 3532 Dihedral : 26.076 161.165 5757 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 2.73 % Allowed : 23.71 % 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: -1.21 (0.17), residues: 2266 helix: 0.46 (0.19), residues: 746 sheet: -1.07 (0.28), residues: 341 loop : -1.57 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 116 TYR 0.025 0.001 TYR G 57 PHE 0.018 0.001 PHE N 10 TRP 0.009 0.001 TRP N 95 HIS 0.011 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00439 (25525) covalent geometry : angle 0.63002 (35762) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.92756 ( 2) hydrogen bonds : bond 0.05194 ( 940) hydrogen bonds : angle 4.16958 ( 2373) metal coordination : bond 0.00598 ( 3) Misc. bond : bond 0.00508 ( 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: 55 poor density : 156 time to evaluate : 0.718 Fit side-chains REVERT: A 97 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 84 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8531 (tp-100) REVERT: K 37 SER cc_start: 0.7191 (OUTLIER) cc_final: 0.6635 (t) REVERT: K 130 MET cc_start: 0.7280 (mmt) cc_final: 0.6999 (mmt) REVERT: K 194 ASP cc_start: 0.7387 (p0) cc_final: 0.7117 (t70) REVERT: K 254 TYR cc_start: 0.6930 (m-80) cc_final: 0.5849 (m-10) REVERT: M 873 TYR cc_start: 0.8275 (m-80) cc_final: 0.8001 (m-80) REVERT: M 939 CYS cc_start: 0.7397 (m) cc_final: 0.7152 (t) REVERT: M 959 TYR cc_start: 0.7970 (m-80) cc_final: 0.7356 (m-80) REVERT: Q 67 LEU cc_start: 0.7543 (mp) cc_final: 0.7262 (mp) REVERT: X 203 ASP cc_start: 0.8798 (t0) cc_final: 0.8447 (m-30) REVERT: L 86 ASP cc_start: 0.4808 (OUTLIER) cc_final: 0.4581 (t0) REVERT: L 203 MET cc_start: 0.7643 (mmp) cc_final: 0.7441 (mmp) REVERT: L 259 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.5989 (t80) REVERT: O 103 MET cc_start: 0.7023 (tpt) cc_final: 0.6285 (tpp) REVERT: O 121 PHE cc_start: 0.7963 (t80) cc_final: 0.7350 (t80) outliers start: 55 outliers final: 47 residues processed: 202 average time/residue: 0.1477 time to fit residues: 48.3018 Evaluate side-chains 202 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU 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 222 SER Chi-restraints excluded: chain K residue 243 TRP Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain M residue 888 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 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 N residue 403 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 66 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 45 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 259 TYR 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 89 ARG Chi-restraints excluded: chain O residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.098002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068499 restraints weight = 94790.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.069693 restraints weight = 53701.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069910 restraints weight = 36606.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070192 restraints weight = 36332.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070022 restraints weight = 29542.864| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25530 Z= 0.162 Angle : 0.612 12.258 35764 Z= 0.337 Chirality : 0.041 0.187 4040 Planarity : 0.004 0.065 3532 Dihedral : 26.000 158.632 5756 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 2.73 % Allowed : 23.61 % Favored : 73.66 % 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: -1.11 (0.17), residues: 2266 helix: 0.59 (0.19), residues: 747 sheet: -1.01 (0.28), residues: 343 loop : -1.55 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.023 0.001 TYR G 57 PHE 0.018 0.001 PHE N 10 TRP 0.008 0.001 TRP N 95 HIS 0.006 0.001 HIS L 325 Details of bonding type rmsd covalent geometry : bond 0.00362 (25525) covalent geometry : angle 0.61228 (35762) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.74398 ( 2) hydrogen bonds : bond 0.04981 ( 940) hydrogen bonds : angle 4.12589 ( 2373) metal coordination : bond 0.00607 ( 3) Misc. bond : bond 0.00390 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4608.21 seconds wall clock time: 80 minutes 8.07 seconds (4808.07 seconds total)