Starting phenix.real_space_refine on Sat Sep 12 04:10:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6muo_9250/09_2026/6muo_9250.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 16 5.16 5 C 7954 2.51 5 N 2578 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14015 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 642 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3027 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 169 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "L" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "M" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1697 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.91, per 1000 atoms: 0.21 Number of scatterers: 14015 At special positions: 0 Unit cell: (121.9, 126.14, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 292 15.00 O 3175 8.00 N 2578 7.00 C 7954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 417.1 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 57.3% alpha, 4.3% beta 71 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.948A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 removed outlier: 3.593A pdb=" N ALA A 71 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.686A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 4.040A pdb=" N ALA A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.516A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.544A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.748A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.843A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.633A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.505A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 removed outlier: 3.539A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.534A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.899A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.933A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.658A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 65 through 84 removed outlier: 4.953A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 103 through 123 removed outlier: 4.033A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.537A pdb=" N GLU E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.878A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.672A pdb=" N GLN E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 111 removed outlier: 4.664A pdb=" N VAL E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.705A pdb=" N HIS E 115 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 117 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.555A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 removed outlier: 4.434A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.937A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.182A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 removed outlier: 4.145A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.823A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.870A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.744A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.748A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 103 through 115 removed outlier: 3.961A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 123 removed outlier: 3.677A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 4.238A pdb=" N GLU M 7 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 14 " --> pdb=" O LYS M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 29 removed outlier: 3.566A pdb=" N LEU M 25 " --> pdb=" O LEU M 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 Processing helix chain 'M' and resid 44 through 58 removed outlier: 3.837A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU M 58 " --> pdb=" O HIS M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 76 removed outlier: 3.553A pdb=" N LEU M 68 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 107 removed outlier: 4.218A pdb=" N SER M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 181 Processing helix chain 'M' and resid 205 through 210 removed outlier: 3.505A pdb=" N ASN M 210 " --> pdb=" O PHE M 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.816A pdb=" N ASN A 85 " --> 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 'B' and resid 96 through 97 removed outlier: 6.791A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.736A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.186A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'M' and resid 125 through 126 removed outlier: 3.754A pdb=" N TYR M 154 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE M 133 " --> pdb=" O VAL M 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL M 152 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP M 137 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LYS M 148 " --> pdb=" O TRP M 137 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR M 151 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR M 155 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR M 160 " --> pdb=" O TYR M 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN M 187 " --> pdb=" O SER M 89 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 162 hydrogen bonds 320 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2570 1.33 - 1.45: 4776 1.45 - 1.57: 6913 1.57 - 1.69: 585 1.69 - 1.80: 30 Bond restraints: 14874 Sorted by residual: bond pdb=" C TYR M 197 " pdb=" N LEU M 198 " ideal model delta sigma weight residual 1.333 1.700 -0.368 1.38e-02 5.25e+03 7.10e+02 bond pdb=" C ASP M 100 " pdb=" N MET M 101 " ideal model delta sigma weight residual 1.333 1.439 -0.106 1.42e-02 4.96e+03 5.58e+01 bond pdb=" C3' DT J -57 " pdb=" C2' DT J -57 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DA J -56 " pdb=" O3' DA J -56 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C3' DA I -32 " pdb=" C2' DA I -32 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 21310 5.36 - 10.73: 39 10.73 - 16.09: 2 16.09 - 21.45: 0 21.45 - 26.82: 2 Bond angle restraints: 21353 Sorted by residual: angle pdb=" O ASP M 100 " pdb=" C ASP M 100 " pdb=" N MET M 101 " ideal model delta sigma weight residual 122.20 147.84 -25.64 1.18e+00 7.18e-01 4.72e+02 angle pdb=" CA ASP M 100 " pdb=" C ASP M 100 " pdb=" N MET M 101 " ideal model delta sigma weight residual 118.59 91.77 26.82 1.28e+00 6.10e-01 4.39e+02 angle pdb=" C ASP M 100 " pdb=" N MET M 101 " pdb=" CA MET M 101 " ideal model delta sigma weight residual 122.34 110.44 11.90 1.39e+00 5.18e-01 7.33e+01 angle pdb=" N PRO G 117 " pdb=" CA PRO G 117 " pdb=" CB PRO G 117 " ideal model delta sigma weight residual 103.00 110.25 -7.25 1.10e+00 8.26e-01 4.34e+01 angle pdb=" O4' DG J 57 " pdb=" C4' DG J 57 " pdb=" C3' DG J 57 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 6881 35.98 - 71.96: 1321 71.96 - 107.93: 33 107.93 - 143.91: 0 143.91 - 179.89: 1 Dihedral angle restraints: 8236 sinusoidal: 5319 harmonic: 2917 Sorted by residual: dihedral pdb=" CA VAL B 21 " pdb=" C VAL B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta harmonic sigma weight residual -180.00 -140.77 -39.23 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA ARG K 526 " pdb=" C ARG K 526 " pdb=" N PRO K 527 " pdb=" CA PRO K 527 " ideal model delta harmonic sigma weight residual -180.00 -149.23 -30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA ALA F 76 " pdb=" C ALA F 76 " pdb=" N LYS F 77 " pdb=" CA LYS F 77 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1817 0.060 - 0.119: 508 0.119 - 0.179: 85 0.179 - 0.239: 4 0.239 - 0.298: 4 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CB VAL B 21 " pdb=" CA VAL B 21 " pdb=" CG1 VAL B 21 " pdb=" CG2 VAL B 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' DT I 58 " pdb=" C4' DT I 58 " pdb=" O3' DT I 58 " pdb=" C2' DT I 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL B 60 " pdb=" CA VAL B 60 " pdb=" CG1 VAL B 60 " pdb=" CG2 VAL B 60 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2415 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP M 100 " -0.015 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ASP M 100 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP M 100 " -0.036 2.00e-02 2.50e+03 pdb=" N MET M 101 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 197 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR M 197 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR M 197 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU M 198 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 21 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C VAL B 21 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL B 21 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 22 " -0.015 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 211 2.64 - 3.21: 11576 3.21 - 3.77: 25408 3.77 - 4.34: 32176 4.34 - 4.90: 44689 Nonbonded interactions: 114060 Sorted by model distance: nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.077 3.120 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.116 3.120 nonbonded pdb=" OD2 ASP M 70 " pdb=" OH TYR M 151 " model vdw 2.129 3.040 nonbonded pdb=" NH1 ARG A 130 " pdb=" O TRP L 531 " model vdw 2.151 3.120 nonbonded pdb=" NH1 ARG B 23 " pdb=" OP1 DT J 16 " model vdw 2.157 3.120 ... (remaining 114055 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 520 through 537) selection = chain 'L' } 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=1.00 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.140 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 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 : 0.009 0.368 14874 Z= 0.651 Angle : 1.051 26.818 21353 Z= 0.815 Chirality : 0.056 0.298 2418 Planarity : 0.006 0.062 1677 Dihedral : 26.213 179.887 6346 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.48 % Allowed : 4.70 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.10 % 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: -6.10 (0.17), residues: 979 helix: -4.59 (0.09), residues: 553 sheet: -2.18 (0.84), residues: 28 loop : -3.09 (0.25), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 69 TYR 0.024 0.003 TYR F 98 PHE 0.019 0.003 PHE A 84 TRP 0.031 0.004 TRP K 531 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.65 (14874) covalent geometry : angle 1.05095 / 0.81 (21353) hydrogen bonds : bond 0.31499 / 20.40 ( 451) hydrogen bonds : angle 11.35678 / 7.76 ( 1181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 343 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7726 (tttt) cc_final: 0.7513 (ttpt) REVERT: A 92 LEU cc_start: 0.7927 (mt) cc_final: 0.7084 (tt) REVERT: B 27 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7400 (mm-40) REVERT: C 39 TYR cc_start: 0.8616 (m-80) cc_final: 0.8278 (m-80) REVERT: C 41 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7405 (tt0) REVERT: C 72 ASP cc_start: 0.8910 (t70) cc_final: 0.8573 (m-30) REVERT: C 100 VAL cc_start: 0.9453 (t) cc_final: 0.9225 (p) REVERT: D 52 THR cc_start: 0.9091 (m) cc_final: 0.8685 (p) REVERT: D 86 ARG cc_start: 0.6977 (mpt-90) cc_final: 0.6225 (mtp180) REVERT: D 106 LEU cc_start: 0.8220 (tp) cc_final: 0.7866 (tt) REVERT: E 65 LEU cc_start: 0.7881 (tp) cc_final: 0.7645 (tt) REVERT: E 80 ARG cc_start: 0.8762 (pmt170) cc_final: 0.7806 (mmt90) REVERT: E 92 LEU cc_start: 0.8109 (mt) cc_final: 0.7839 (tt) REVERT: E 104 HIS cc_start: 0.8239 (t70) cc_final: 0.7724 (t70) REVERT: E 136 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7903 (mm-30) REVERT: F 44 LYS cc_start: 0.7663 (tttt) cc_final: 0.7457 (tttt) REVERT: G 23 LEU cc_start: 0.8595 (mt) cc_final: 0.8262 (mp) REVERT: G 36 LYS cc_start: 0.8128 (mmpt) cc_final: 0.7586 (tttm) REVERT: G 38 ASN cc_start: 0.8894 (m-40) cc_final: 0.8173 (p0) REVERT: G 41 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7989 (tm-30) REVERT: G 99 ARG cc_start: 0.7506 (mmt180) cc_final: 0.6497 (mtm180) REVERT: H 62 MET cc_start: 0.8296 (mmm) cc_final: 0.7771 (mmp) REVERT: H 71 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 93 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8030 (mt-10) REVERT: H 105 GLU cc_start: 0.8464 (tp30) cc_final: 0.8259 (tp30) REVERT: K 536 GLU cc_start: 0.3731 (OUTLIER) cc_final: 0.3213 (pm20) REVERT: L 523 ILE cc_start: 0.7806 (mp) cc_final: 0.7433 (mp) REVERT: M 17 PRO cc_start: 0.8422 (Cg_exo) cc_final: 0.8221 (Cg_endo) REVERT: M 74 MET cc_start: 0.8677 (tpp) cc_final: 0.8398 (tpt) REVERT: M 79 HIS cc_start: 0.8565 (p-80) cc_final: 0.7962 (m90) REVERT: M 131 VAL cc_start: 0.7689 (p) cc_final: 0.7351 (m) REVERT: M 133 ILE cc_start: 0.6148 (mt) cc_final: 0.5613 (tp) REVERT: M 135 ILE cc_start: 0.8995 (mp) cc_final: 0.8750 (mm) REVERT: M 153 VAL cc_start: 0.7962 (t) cc_final: 0.7751 (t) REVERT: M 162 PHE cc_start: 0.8953 (m-10) cc_final: 0.8611 (m-80) REVERT: M 171 ASN cc_start: 0.8203 (t160) cc_final: 0.7545 (t0) REVERT: M 181 ILE cc_start: 0.9039 (mt) cc_final: 0.8805 (pt) REVERT: M 191 MET cc_start: 0.6507 (mtt) cc_final: 0.6038 (mpp) outliers start: 4 outliers final: 1 residues processed: 346 average time/residue: 0.1506 time to fit residues: 70.4331 Evaluate side-chains 219 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain K residue 536 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN B 93 GLN C 94 ASN C 110 ASN D 82 HIS D 109 HIS E 59 HIS G 31 HIS G 73 ASN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN M 145 ASN M 146 GLN M 157 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083737 restraints weight = 22530.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087206 restraints weight = 10515.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089454 restraints weight = 6792.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090933 restraints weight = 5292.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091756 restraints weight = 4591.299| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14874 Z= 0.204 Angle : 0.854 11.088 21353 Z= 0.476 Chirality : 0.054 0.449 2418 Planarity : 0.006 0.069 1677 Dihedral : 30.605 168.560 4415 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.61 % Allowed : 13.49 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.80 (0.20), residues: 979 helix: -3.29 (0.15), residues: 568 sheet: -1.63 (0.91), residues: 28 loop : -2.88 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 80 TYR 0.021 0.002 TYR M 151 PHE 0.016 0.002 PHE B 100 TRP 0.013 0.002 TRP M 137 HIS 0.012 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 (14874) covalent geometry : angle 0.85363 / 0.48 (21353) hydrogen bonds : bond 0.08803 / 5.78 ( 451) hydrogen bonds : angle 4.92069 / 3.41 ( 1181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7870 (tttt) cc_final: 0.7507 (ttpt) REVERT: A 92 LEU cc_start: 0.7820 (mt) cc_final: 0.7109 (tt) REVERT: A 125 ASP cc_start: 0.8279 (m-30) cc_final: 0.8012 (m-30) REVERT: B 27 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7593 (mm-40) REVERT: B 40 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: B 75 HIS cc_start: 0.9054 (t-90) cc_final: 0.8634 (t-170) REVERT: C 41 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7359 (tt0) REVERT: D 52 THR cc_start: 0.9138 (m) cc_final: 0.8597 (p) REVERT: D 86 ARG cc_start: 0.7070 (mpt-90) cc_final: 0.6395 (mtp180) REVERT: E 65 LEU cc_start: 0.8067 (tp) cc_final: 0.7826 (tt) REVERT: E 80 ARG cc_start: 0.8682 (pmt170) cc_final: 0.7756 (mmt90) REVERT: E 92 LEU cc_start: 0.8176 (mt) cc_final: 0.7901 (tt) REVERT: E 104 HIS cc_start: 0.8351 (t70) cc_final: 0.7814 (t70) REVERT: E 136 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 137 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7092 (mm-30) REVERT: G 20 ARG cc_start: 0.9292 (ttt180) cc_final: 0.9008 (ttp80) REVERT: G 36 LYS cc_start: 0.7958 (mmpt) cc_final: 0.7442 (tttm) REVERT: G 38 ASN cc_start: 0.8969 (m-40) cc_final: 0.8318 (p0) REVERT: G 41 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 56 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7478 (tm-30) REVERT: H 62 MET cc_start: 0.8410 (mmm) cc_final: 0.8021 (mmp) REVERT: H 71 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8007 (tm-30) REVERT: H 93 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7845 (mt-10) REVERT: M 18 MET cc_start: 0.8913 (mmm) cc_final: 0.8663 (mmm) REVERT: M 50 GLN cc_start: 0.7968 (mt0) cc_final: 0.7700 (tt0) REVERT: M 51 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7750 (t-90) REVERT: M 79 HIS cc_start: 0.8406 (p-80) cc_final: 0.7739 (m90) REVERT: M 133 ILE cc_start: 0.6020 (mt) cc_final: 0.5741 (tp) REVERT: M 151 TYR cc_start: 0.7695 (m-80) cc_final: 0.7410 (m-10) REVERT: M 162 PHE cc_start: 0.9101 (m-10) cc_final: 0.8698 (m-80) REVERT: M 171 ASN cc_start: 0.7642 (t160) cc_final: 0.6844 (t0) REVERT: M 191 MET cc_start: 0.5947 (mtt) cc_final: 0.5679 (mpp) outliers start: 30 outliers final: 17 residues processed: 258 average time/residue: 0.1291 time to fit residues: 47.3145 Evaluate side-chains 216 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS E 104 HIS H 47 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082042 restraints weight = 23766.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085489 restraints weight = 10754.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087674 restraints weight = 6853.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088992 restraints weight = 5319.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089770 restraints weight = 4636.206| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 14874 Z= 0.390 Angle : 0.989 10.689 21353 Z= 0.535 Chirality : 0.057 0.329 2418 Planarity : 0.008 0.074 1677 Dihedral : 30.756 147.383 4410 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 6.99 % Allowed : 16.14 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.98 (0.24), residues: 979 helix: -2.49 (0.18), residues: 567 sheet: -1.21 (0.85), residues: 28 loop : -2.78 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 80 TYR 0.038 0.004 TYR D 40 PHE 0.016 0.003 PHE E 67 TRP 0.039 0.004 TRP M 28 HIS 0.011 0.002 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.39 (14874) covalent geometry : angle 0.98860 / 0.53 (21353) hydrogen bonds : bond 0.08348 / 5.51 ( 451) hydrogen bonds : angle 5.31216 / 3.63 ( 1181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7993 (tttt) cc_final: 0.7647 (ttpt) REVERT: A 92 LEU cc_start: 0.7866 (mt) cc_final: 0.7048 (tt) REVERT: A 110 TYR cc_start: 0.8043 (t80) cc_final: 0.7767 (t80) REVERT: C 24 GLN cc_start: 0.8578 (mm-40) cc_final: 0.7914 (mp10) REVERT: C 41 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7897 (tt0) REVERT: C 56 GLU cc_start: 0.7398 (tt0) cc_final: 0.7066 (tt0) REVERT: C 90 ASP cc_start: 0.8005 (t70) cc_final: 0.7473 (t70) REVERT: D 52 THR cc_start: 0.9079 (m) cc_final: 0.8493 (p) REVERT: D 86 ARG cc_start: 0.7318 (mpt-90) cc_final: 0.6509 (mtp180) REVERT: E 65 LEU cc_start: 0.8168 (tp) cc_final: 0.7946 (tt) REVERT: E 80 ARG cc_start: 0.8725 (pmt170) cc_final: 0.7710 (mmt90) REVERT: E 92 LEU cc_start: 0.8157 (mt) cc_final: 0.7859 (tt) REVERT: E 95 GLN cc_start: 0.8367 (tt0) cc_final: 0.8081 (tt0) REVERT: E 96 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8660 (tp30) REVERT: E 108 ASP cc_start: 0.8920 (t0) cc_final: 0.8652 (t70) REVERT: E 135 LEU cc_start: 0.7644 (tt) cc_final: 0.7011 (tt) REVERT: E 136 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8059 (mm-30) REVERT: F 98 TYR cc_start: 0.8544 (m-10) cc_final: 0.8256 (m-80) REVERT: G 20 ARG cc_start: 0.9323 (ttt180) cc_final: 0.9043 (tpt-90) REVERT: G 36 LYS cc_start: 0.8101 (mmpt) cc_final: 0.7592 (tmtt) REVERT: G 41 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8036 (tm-30) REVERT: G 56 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7501 (tm-30) REVERT: G 99 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7046 (mtm180) REVERT: H 59 MET cc_start: 0.7665 (tpp) cc_final: 0.7423 (tpp) REVERT: H 93 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7579 (mt-10) REVERT: M 50 GLN cc_start: 0.7960 (mt0) cc_final: 0.7694 (tt0) REVERT: M 51 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: M 74 MET cc_start: 0.9130 (tpt) cc_final: 0.8762 (tpt) REVERT: M 79 HIS cc_start: 0.8482 (p-80) cc_final: 0.7759 (m90) REVERT: M 137 TRP cc_start: 0.8679 (m100) cc_final: 0.8360 (m100) REVERT: M 151 TYR cc_start: 0.7587 (m-80) cc_final: 0.7175 (m-10) REVERT: M 162 PHE cc_start: 0.9103 (m-10) cc_final: 0.8645 (m-80) REVERT: M 171 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.6770 (t0) outliers start: 58 outliers final: 42 residues processed: 244 average time/residue: 0.1278 time to fit residues: 44.5780 Evaluate side-chains 234 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 59 HIS H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083860 restraints weight = 23393.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087434 restraints weight = 10303.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089709 restraints weight = 6505.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091065 restraints weight = 5028.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091773 restraints weight = 4390.135| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14874 Z= 0.267 Angle : 0.818 10.325 21353 Z= 0.457 Chirality : 0.050 0.249 2418 Planarity : 0.006 0.077 1677 Dihedral : 30.689 148.301 4410 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 6.99 % Allowed : 19.04 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.55 (0.24), residues: 979 helix: -2.08 (0.19), residues: 570 sheet: -1.06 (0.83), residues: 28 loop : -2.73 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 29 TYR 0.026 0.003 TYR E 110 PHE 0.015 0.002 PHE B 100 TRP 0.013 0.003 TRP M 132 HIS 0.012 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 (14874) covalent geometry : angle 0.81811 / 0.46 (21353) hydrogen bonds : bond 0.06764 / 4.49 ( 451) hydrogen bonds : angle 4.67255 / 3.20 ( 1181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7775 (mt) cc_final: 0.7059 (tt) REVERT: A 137 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6424 (mt-10) REVERT: C 41 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7954 (tt0) REVERT: C 56 GLU cc_start: 0.7468 (tt0) cc_final: 0.7109 (tt0) REVERT: D 52 THR cc_start: 0.8986 (m) cc_final: 0.8378 (p) REVERT: D 86 ARG cc_start: 0.7274 (mpt-90) cc_final: 0.6406 (mtp180) REVERT: E 65 LEU cc_start: 0.8082 (tp) cc_final: 0.7867 (tt) REVERT: E 80 ARG cc_start: 0.8697 (pmt170) cc_final: 0.7625 (mmt90) REVERT: E 92 LEU cc_start: 0.8142 (mt) cc_final: 0.7800 (tt) REVERT: E 95 GLN cc_start: 0.8286 (tt0) cc_final: 0.7988 (tt0) REVERT: E 135 LEU cc_start: 0.7691 (tt) cc_final: 0.7093 (tt) REVERT: E 136 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8042 (mm-30) REVERT: F 29 ILE cc_start: 0.8475 (mm) cc_final: 0.8251 (mm) REVERT: G 20 ARG cc_start: 0.9294 (ttt180) cc_final: 0.8981 (tpt-90) REVERT: G 36 LYS cc_start: 0.7952 (mmpt) cc_final: 0.7421 (tmtt) REVERT: G 41 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8021 (tm-30) REVERT: G 56 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7395 (tm-30) REVERT: G 99 ARG cc_start: 0.8225 (mmt180) cc_final: 0.6927 (mtm180) REVERT: H 93 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7585 (mt-10) REVERT: M 50 GLN cc_start: 0.8075 (mt0) cc_final: 0.7802 (tt0) REVERT: M 51 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: M 74 MET cc_start: 0.9054 (tpt) cc_final: 0.8603 (tpt) REVERT: M 79 HIS cc_start: 0.8443 (p-80) cc_final: 0.7769 (m90) REVERT: M 162 PHE cc_start: 0.9120 (m-10) cc_final: 0.8696 (m-80) REVERT: M 171 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.6811 (t0) outliers start: 58 outliers final: 46 residues processed: 230 average time/residue: 0.1212 time to fit residues: 40.3701 Evaluate side-chains 238 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 59 HIS H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086910 restraints weight = 23068.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090635 restraints weight = 9986.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093007 restraints weight = 6239.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094419 restraints weight = 4809.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095211 restraints weight = 4181.758| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14874 Z= 0.179 Angle : 0.726 9.669 21353 Z= 0.415 Chirality : 0.047 0.236 2418 Planarity : 0.005 0.070 1677 Dihedral : 30.620 147.501 4410 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.86 % Allowed : 24.10 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.21 (0.25), residues: 979 helix: -1.75 (0.20), residues: 572 sheet: -0.89 (0.88), residues: 28 loop : -2.68 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.022 0.002 TYR E 110 PHE 0.017 0.001 PHE B 100 TRP 0.012 0.002 TRP M 132 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (14874) covalent geometry : angle 0.72594 / 0.42 (21353) hydrogen bonds : bond 0.05894 / 3.91 ( 451) hydrogen bonds : angle 4.15810 / 2.87 ( 1181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7612 (mt) cc_final: 0.6988 (tt) REVERT: A 114 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 118 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6661 (mtt180) REVERT: C 41 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7883 (tt0) REVERT: C 56 GLU cc_start: 0.7452 (tt0) cc_final: 0.6565 (tt0) REVERT: C 92 GLU cc_start: 0.8999 (mp0) cc_final: 0.8443 (mp0) REVERT: D 52 THR cc_start: 0.8949 (m) cc_final: 0.8308 (p) REVERT: D 86 ARG cc_start: 0.7192 (mpt-90) cc_final: 0.6400 (mtp180) REVERT: E 65 LEU cc_start: 0.7952 (tp) cc_final: 0.7698 (tt) REVERT: E 80 ARG cc_start: 0.8646 (pmt170) cc_final: 0.7583 (mmt90) REVERT: E 92 LEU cc_start: 0.8148 (mt) cc_final: 0.7937 (tp) REVERT: E 95 GLN cc_start: 0.8207 (tt0) cc_final: 0.7812 (tt0) REVERT: E 128 LEU cc_start: 0.8371 (tp) cc_final: 0.8167 (tt) REVERT: E 135 LEU cc_start: 0.7674 (tt) cc_final: 0.7168 (tt) REVERT: F 29 ILE cc_start: 0.8362 (mm) cc_final: 0.8108 (mm) REVERT: F 92 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.7322 (tmm-80) REVERT: G 20 ARG cc_start: 0.9252 (ttt180) cc_final: 0.8954 (tpt-90) REVERT: G 36 LYS cc_start: 0.7846 (mmpt) cc_final: 0.7348 (tmtt) REVERT: G 41 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8005 (tm-30) REVERT: G 92 GLU cc_start: 0.8696 (mp0) cc_final: 0.8325 (mp0) REVERT: H 93 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7563 (mt-10) REVERT: K 522 ARG cc_start: 0.8492 (ptt90) cc_final: 0.8089 (ptt90) REVERT: M 18 MET cc_start: 0.8541 (mmm) cc_final: 0.8269 (mmm) REVERT: M 51 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7714 (t-90) REVERT: M 74 MET cc_start: 0.9039 (tpt) cc_final: 0.8495 (tpt) REVERT: M 79 HIS cc_start: 0.8385 (p-80) cc_final: 0.7734 (m90) REVERT: M 162 PHE cc_start: 0.9117 (m-10) cc_final: 0.8900 (m-80) REVERT: M 171 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.6765 (t0) outliers start: 32 outliers final: 23 residues processed: 215 average time/residue: 0.1240 time to fit residues: 38.6697 Evaluate side-chains 216 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 45 GLN E 59 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085122 restraints weight = 24338.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088299 restraints weight = 12147.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090348 restraints weight = 8177.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091587 restraints weight = 6540.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092260 restraints weight = 5781.247| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14874 Z= 0.222 Angle : 0.757 9.762 21353 Z= 0.426 Chirality : 0.047 0.232 2418 Planarity : 0.005 0.068 1677 Dihedral : 30.598 147.011 4410 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 6.51 % Allowed : 22.77 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.03 (0.25), residues: 979 helix: -1.62 (0.21), residues: 572 sheet: -0.99 (0.87), residues: 28 loop : -2.57 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.033 0.002 TYR F 88 PHE 0.015 0.001 PHE B 100 TRP 0.017 0.002 TRP M 28 HIS 0.012 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (14874) covalent geometry : angle 0.75669 / 0.43 (21353) hydrogen bonds : bond 0.05840 / 3.86 ( 451) hydrogen bonds : angle 4.25386 / 2.92 ( 1181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8104 (mt) cc_final: 0.7378 (tt) REVERT: A 108 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8245 (t0) REVERT: A 118 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: B 25 ASN cc_start: 0.7863 (t0) cc_final: 0.7449 (t0) REVERT: C 41 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7927 (tt0) REVERT: C 56 GLU cc_start: 0.7856 (tt0) cc_final: 0.6843 (tt0) REVERT: C 92 GLU cc_start: 0.9046 (mp0) cc_final: 0.8592 (mp0) REVERT: D 52 THR cc_start: 0.9204 (m) cc_final: 0.8602 (p) REVERT: D 86 ARG cc_start: 0.7433 (mpt-90) cc_final: 0.6700 (mtp180) REVERT: D 98 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (p) REVERT: E 65 LEU cc_start: 0.8409 (tp) cc_final: 0.8163 (tt) REVERT: E 80 ARG cc_start: 0.8553 (pmt170) cc_final: 0.7670 (mmt90) REVERT: E 92 LEU cc_start: 0.8538 (mt) cc_final: 0.8258 (tt) REVERT: F 29 ILE cc_start: 0.8641 (mm) cc_final: 0.8353 (mm) REVERT: F 44 LYS cc_start: 0.8083 (tttt) cc_final: 0.7609 (tptm) REVERT: F 92 ARG cc_start: 0.8188 (tmm-80) cc_final: 0.7595 (tmm-80) REVERT: G 20 ARG cc_start: 0.9282 (ttt180) cc_final: 0.8965 (tpt-90) REVERT: G 36 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7699 (tmtt) REVERT: G 41 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8089 (tm-30) REVERT: G 85 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8232 (tt) REVERT: G 92 GLU cc_start: 0.8809 (mp0) cc_final: 0.8553 (mp0) REVERT: G 99 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7245 (mtm180) REVERT: H 93 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7693 (mt-10) REVERT: M 28 TRP cc_start: 0.8101 (t60) cc_final: 0.7826 (t60) REVERT: M 51 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (t-90) REVERT: M 74 MET cc_start: 0.9055 (tpt) cc_final: 0.8511 (tpt) REVERT: M 79 HIS cc_start: 0.8526 (p-80) cc_final: 0.7852 (m90) REVERT: M 162 PHE cc_start: 0.9050 (m-10) cc_final: 0.8800 (m-80) REVERT: M 171 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.6777 (t0) outliers start: 54 outliers final: 38 residues processed: 224 average time/residue: 0.1217 time to fit residues: 39.6552 Evaluate side-chains 231 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 38 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088551 restraints weight = 24028.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091876 restraints weight = 11859.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094035 restraints weight = 7920.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095358 restraints weight = 6308.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096092 restraints weight = 5565.532| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 14874 Z= 0.144 Angle : 0.683 10.823 21353 Z= 0.392 Chirality : 0.044 0.223 2418 Planarity : 0.005 0.063 1677 Dihedral : 30.494 146.929 4410 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.70 % Allowed : 24.70 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.67 (0.26), residues: 979 helix: -1.34 (0.21), residues: 572 sheet: -1.02 (0.83), residues: 28 loop : -2.39 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 92 TYR 0.022 0.002 TYR A 110 PHE 0.017 0.001 PHE B 100 TRP 0.014 0.002 TRP M 132 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14874) covalent geometry : angle 0.68343 / 0.39 (21353) hydrogen bonds : bond 0.05153 / 3.39 ( 451) hydrogen bonds : angle 3.71999 / 2.56 ( 1181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6980 (ptp90) REVERT: A 108 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7959 (t0) REVERT: B 29 ILE cc_start: 0.8653 (mm) cc_final: 0.8384 (mm) REVERT: C 39 TYR cc_start: 0.8391 (m-80) cc_final: 0.8140 (m-80) REVERT: C 41 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7555 (tt0) REVERT: C 51 LEU cc_start: 0.7637 (tp) cc_final: 0.7415 (tt) REVERT: C 56 GLU cc_start: 0.7699 (tt0) cc_final: 0.6808 (tt0) REVERT: C 92 GLU cc_start: 0.9037 (mp0) cc_final: 0.8369 (mp0) REVERT: D 86 ARG cc_start: 0.7392 (mpt-90) cc_final: 0.6639 (mtp180) REVERT: E 65 LEU cc_start: 0.8205 (tp) cc_final: 0.8004 (tt) REVERT: E 80 ARG cc_start: 0.8511 (pmt170) cc_final: 0.7578 (mmt90) REVERT: E 96 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8100 (mm-30) REVERT: F 29 ILE cc_start: 0.8574 (mm) cc_final: 0.8265 (mm) REVERT: F 44 LYS cc_start: 0.7908 (tttt) cc_final: 0.7548 (tptm) REVERT: F 92 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7464 (tmm-80) REVERT: G 20 ARG cc_start: 0.9238 (ttt180) cc_final: 0.8911 (tpt-90) REVERT: G 36 LYS cc_start: 0.8096 (mmpt) cc_final: 0.7582 (tmtt) REVERT: G 38 ASN cc_start: 0.8984 (m-40) cc_final: 0.8379 (p0) REVERT: G 41 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8065 (tm-30) REVERT: G 85 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8048 (tt) REVERT: H 93 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7798 (mt-10) REVERT: M 18 MET cc_start: 0.8661 (mmm) cc_final: 0.8360 (mmm) REVERT: M 51 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7788 (t-90) REVERT: M 74 MET cc_start: 0.9072 (tpt) cc_final: 0.8498 (tpt) REVERT: M 79 HIS cc_start: 0.8356 (p-80) cc_final: 0.7640 (m90) REVERT: M 162 PHE cc_start: 0.9056 (m-10) cc_final: 0.8812 (m-80) REVERT: M 171 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.6666 (t0) outliers start: 39 outliers final: 19 residues processed: 222 average time/residue: 0.1293 time to fit residues: 41.2125 Evaluate side-chains 208 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN C 38 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 59 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.150080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088337 restraints weight = 23945.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091629 restraints weight = 11989.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093705 restraints weight = 8062.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095066 restraints weight = 6462.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095663 restraints weight = 5699.522| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14874 Z= 0.149 Angle : 0.683 11.758 21353 Z= 0.389 Chirality : 0.043 0.225 2418 Planarity : 0.004 0.058 1677 Dihedral : 30.461 146.840 4410 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.86 % Allowed : 26.63 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.46 (0.26), residues: 979 helix: -1.15 (0.21), residues: 571 sheet: -0.92 (0.83), residues: 28 loop : -2.31 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.020 0.002 TYR H 83 PHE 0.015 0.001 PHE B 100 TRP 0.027 0.002 TRP M 28 HIS 0.013 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14874) covalent geometry : angle 0.68316 / 0.39 (21353) hydrogen bonds : bond 0.04976 / 3.27 ( 451) hydrogen bonds : angle 3.64664 / 2.50 ( 1181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7206 (ptp90) cc_final: 0.6949 (ptp90) REVERT: A 108 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 29 ILE cc_start: 0.8617 (mm) cc_final: 0.8276 (mm) REVERT: C 41 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7523 (tt0) REVERT: C 56 GLU cc_start: 0.7695 (tt0) cc_final: 0.6782 (tt0) REVERT: C 92 GLU cc_start: 0.9074 (mp0) cc_final: 0.8424 (mp0) REVERT: D 52 THR cc_start: 0.9215 (m) cc_final: 0.8706 (p) REVERT: D 86 ARG cc_start: 0.7229 (mpt-90) cc_final: 0.6454 (mtp180) REVERT: E 80 ARG cc_start: 0.8577 (pmt170) cc_final: 0.7598 (mmt90) REVERT: E 96 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8013 (mm-30) REVERT: F 29 ILE cc_start: 0.8574 (mm) cc_final: 0.8213 (mm) REVERT: F 92 ARG cc_start: 0.8111 (tmm-80) cc_final: 0.7458 (tmm-80) REVERT: G 20 ARG cc_start: 0.9235 (ttt180) cc_final: 0.8903 (tpt-90) REVERT: G 36 LYS cc_start: 0.8102 (mmpt) cc_final: 0.7598 (tmtt) REVERT: G 38 ASN cc_start: 0.8946 (m-40) cc_final: 0.8582 (p0) REVERT: G 41 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8059 (tm-30) REVERT: G 85 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8057 (tt) REVERT: H 93 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7828 (mt-10) REVERT: M 18 MET cc_start: 0.8531 (mmm) cc_final: 0.8221 (mmm) REVERT: M 51 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7791 (t-90) REVERT: M 74 MET cc_start: 0.9069 (tpt) cc_final: 0.8791 (tpt) REVERT: M 79 HIS cc_start: 0.8404 (p-80) cc_final: 0.7684 (m90) REVERT: M 137 TRP cc_start: 0.8663 (m100) cc_final: 0.8313 (m100) REVERT: M 162 PHE cc_start: 0.9006 (m-10) cc_final: 0.8778 (m-80) REVERT: M 171 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.6953 (t0) outliers start: 32 outliers final: 24 residues processed: 207 average time/residue: 0.1212 time to fit residues: 36.8596 Evaluate side-chains 212 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS G 84 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089635 restraints weight = 23826.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.092943 restraints weight = 11943.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095041 restraints weight = 8049.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096398 restraints weight = 6454.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097175 restraints weight = 5697.459| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14874 Z= 0.140 Angle : 0.664 12.236 21353 Z= 0.379 Chirality : 0.042 0.212 2418 Planarity : 0.004 0.053 1677 Dihedral : 30.362 145.881 4410 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.98 % Allowed : 26.99 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.17 (0.26), residues: 979 helix: -0.89 (0.21), residues: 571 sheet: -0.04 (0.87), residues: 26 loop : -2.29 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 60 TYR 0.034 0.002 TYR M 73 PHE 0.014 0.001 PHE F 100 TRP 0.024 0.002 TRP M 28 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14874) covalent geometry : angle 0.66391 / 0.38 (21353) hydrogen bonds : bond 0.04730 / 3.11 ( 451) hydrogen bonds : angle 3.52181 / 2.42 ( 1181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6888 (ptp90) REVERT: A 108 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7848 (t0) REVERT: B 29 ILE cc_start: 0.8572 (mm) cc_final: 0.8197 (mm) REVERT: C 41 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7617 (tt0) REVERT: C 56 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: C 64 GLU cc_start: 0.7749 (tt0) cc_final: 0.7238 (tm-30) REVERT: C 92 GLU cc_start: 0.9078 (mp0) cc_final: 0.8444 (mp0) REVERT: D 52 THR cc_start: 0.9194 (m) cc_final: 0.8511 (p) REVERT: D 86 ARG cc_start: 0.7187 (mpt-90) cc_final: 0.6411 (mtp180) REVERT: E 80 ARG cc_start: 0.8606 (pmt170) cc_final: 0.7595 (mmt90) REVERT: E 96 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8069 (mm-30) REVERT: F 44 LYS cc_start: 0.7826 (tttt) cc_final: 0.7220 (mmmt) REVERT: F 88 TYR cc_start: 0.7528 (m-10) cc_final: 0.7270 (m-80) REVERT: F 92 ARG cc_start: 0.8139 (tmm-80) cc_final: 0.7473 (tmm-80) REVERT: F 98 TYR cc_start: 0.8560 (m-10) cc_final: 0.8251 (m-80) REVERT: G 20 ARG cc_start: 0.9212 (ttt180) cc_final: 0.8867 (tpt-90) REVERT: G 36 LYS cc_start: 0.8031 (mmpt) cc_final: 0.7528 (tmtt) REVERT: G 38 ASN cc_start: 0.9000 (m-40) cc_final: 0.8712 (p0) REVERT: G 41 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8009 (tm-30) REVERT: G 85 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7937 (tt) REVERT: H 82 HIS cc_start: 0.8505 (t-170) cc_final: 0.8046 (t-90) REVERT: H 93 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7938 (mt-10) REVERT: M 1 MET cc_start: 0.0820 (mpp) cc_final: -0.0948 (tpt) REVERT: M 18 MET cc_start: 0.8541 (mmm) cc_final: 0.8235 (mmm) REVERT: M 51 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (t-90) REVERT: M 74 MET cc_start: 0.9079 (tpt) cc_final: 0.8775 (tpt) REVERT: M 79 HIS cc_start: 0.8332 (p-80) cc_final: 0.7542 (m90) REVERT: M 162 PHE cc_start: 0.9051 (m-10) cc_final: 0.8827 (m-80) REVERT: M 171 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6798 (t0) outliers start: 33 outliers final: 22 residues processed: 201 average time/residue: 0.1206 time to fit residues: 35.4558 Evaluate side-chains 205 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 56 CYS Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS E 95 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089313 restraints weight = 23764.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092619 restraints weight = 11916.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094760 restraints weight = 8042.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096059 restraints weight = 6433.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096842 restraints weight = 5692.535| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.145 Angle : 0.661 11.670 21353 Z= 0.376 Chirality : 0.042 0.208 2418 Planarity : 0.004 0.051 1677 Dihedral : 30.317 145.102 4410 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.13 % Allowed : 27.71 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.26), residues: 979 helix: -0.76 (0.22), residues: 575 sheet: 0.21 (0.89), residues: 26 loop : -2.29 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 131 TYR 0.027 0.002 TYR M 73 PHE 0.013 0.001 PHE F 100 TRP 0.024 0.002 TRP M 28 HIS 0.009 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (14874) covalent geometry : angle 0.66090 / 0.38 (21353) hydrogen bonds : bond 0.04626 / 3.05 ( 451) hydrogen bonds : angle 3.54347 / 2.43 ( 1181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7242 (ptp90) cc_final: 0.6938 (ptp90) REVERT: A 108 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7876 (t0) REVERT: B 29 ILE cc_start: 0.8519 (mm) cc_final: 0.8160 (mm) REVERT: C 41 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7624 (tt0) REVERT: C 56 GLU cc_start: 0.7886 (tt0) cc_final: 0.6999 (tt0) REVERT: C 92 GLU cc_start: 0.9084 (mp0) cc_final: 0.8439 (mp0) REVERT: D 52 THR cc_start: 0.9171 (m) cc_final: 0.8490 (p) REVERT: D 86 ARG cc_start: 0.7215 (mpt-90) cc_final: 0.6357 (mtp180) REVERT: E 96 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8101 (mm-30) REVERT: F 92 ARG cc_start: 0.8310 (tmm-80) cc_final: 0.8096 (tmm-80) REVERT: G 20 ARG cc_start: 0.9219 (ttt180) cc_final: 0.8874 (tpt-90) REVERT: G 36 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7543 (tmtt) REVERT: G 38 ASN cc_start: 0.9007 (m-40) cc_final: 0.8726 (p0) REVERT: G 41 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8014 (tm-30) REVERT: G 56 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7653 (tm-30) REVERT: G 85 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7828 (tt) REVERT: H 93 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7916 (mt-10) REVERT: M 1 MET cc_start: 0.1038 (mpp) cc_final: -0.0859 (tpt) REVERT: M 18 MET cc_start: 0.8519 (mmm) cc_final: 0.8215 (mmm) REVERT: M 51 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7738 (t-90) REVERT: M 74 MET cc_start: 0.9083 (tpt) cc_final: 0.8804 (tpt) REVERT: M 79 HIS cc_start: 0.8353 (p-80) cc_final: 0.7544 (m90) REVERT: M 137 TRP cc_start: 0.8635 (m100) cc_final: 0.8282 (m100) REVERT: M 162 PHE cc_start: 0.9051 (m-10) cc_final: 0.8819 (m-80) REVERT: M 171 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6934 (t0) outliers start: 26 outliers final: 21 residues processed: 195 average time/residue: 0.1213 time to fit residues: 34.6172 Evaluate side-chains 203 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 116 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN E 59 HIS H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091471 restraints weight = 23693.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094899 restraints weight = 11681.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097150 restraints weight = 7813.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098468 restraints weight = 6215.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099300 restraints weight = 5494.257| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14874 Z= 0.134 Angle : 0.648 11.597 21353 Z= 0.371 Chirality : 0.041 0.202 2418 Planarity : 0.004 0.077 1677 Dihedral : 30.203 144.485 4410 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.77 % Allowed : 28.19 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 979 helix: -0.59 (0.22), residues: 573 sheet: 0.49 (0.93), residues: 26 loop : -2.27 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.029 0.002 TYR M 73 PHE 0.014 0.001 PHE F 100 TRP 0.024 0.001 TRP M 28 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (14874) covalent geometry : angle 0.64801 / 0.37 (21353) hydrogen bonds : bond 0.04409 / 2.90 ( 451) hydrogen bonds : angle 3.41042 / 2.34 ( 1181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.53 seconds wall clock time: 45 minutes 43.98 seconds (2743.98 seconds total)