Starting phenix.real_space_refine on Wed Mar 4 12:31:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6muo_9250/03_2026/6muo_9250_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6muo_9250/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6muo_9250/03_2026/6muo_9250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6muo_9250/03_2026/6muo_9250.map" model { file = "/net/cci-nas-00/data/ceres_data/6muo_9250/03_2026/6muo_9250_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6muo_9250/03_2026/6muo_9250_neut.cif" } 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-dev-5986/lib/python3.9/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: 3.00, 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: 0.94 Conformation dependent library (CDL) restraints added in 348.6 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: 1.98 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: 1.99 Time building geometry restraints manager: 1.30 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=" N VAL K 533 " pdb=" CA VAL K 533 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.63e+00 bond pdb=" C ARG K 526 " pdb=" N PRO K 527 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.52e+00 bond pdb=" N SER K 535 " pdb=" CA SER K 535 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 6.96e+00 ... (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=" C ASP A 125 " pdb=" N VAL A 126 " pdb=" CA VAL A 126 " ideal model delta sigma weight residual 122.66 118.43 4.23 9.70e-01 1.06e+00 1.90e+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: 2044 0.060 - 0.119: 317 0.119 - 0.179: 49 0.179 - 0.239: 5 0.239 - 0.298: 3 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=" 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 chirality pdb=" CA PRO G 117 " pdb=" N PRO G 117 " pdb=" C PRO G 117 " pdb=" CB PRO G 117 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+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: 0.670 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.008 0.368 14874 Z= 0.387 Angle : 0.953 26.818 21353 Z= 0.582 Chirality : 0.047 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 covalent geometry : bond 0.00754 (14874) covalent geometry : angle 0.95289 (21353) hydrogen bonds : bond 0.31499 ( 451) hydrogen bonds : angle 11.35678 ( 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 : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7726 (tttt) cc_final: 0.7513 (ttpt) REVERT: A 92 LEU cc_start: 0.7927 (mt) cc_final: 0.7083 (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: 0.7723 (t70) REVERT: E 136 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7904 (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: 0.7772 (mmp) REVERT: H 71 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7588 (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: 0.8222 (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: 0.8612 (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: 0.6037 (mpp) outliers start: 4 outliers final: 1 residues processed: 346 average time/residue: 0.1451 time to fit residues: 67.1453 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 : 0.281 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN B 93 GLN C 94 ASN C 110 ASN D 82 HIS D 109 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 M 177 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093547 restraints weight = 24133.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097192 restraints weight = 11539.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099591 restraints weight = 7569.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100970 restraints weight = 5956.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101912 restraints weight = 5241.563| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14874 Z= 0.174 Angle : 0.673 8.361 21353 Z= 0.394 Chirality : 0.040 0.268 2418 Planarity : 0.005 0.037 1677 Dihedral : 30.224 155.641 4415 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.41 % Allowed : 14.10 % Favored : 83.49 % 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: -4.47 (0.21), residues: 979 helix: -3.01 (0.16), residues: 572 sheet: -1.31 (0.87), residues: 28 loop : -2.77 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.030 0.002 TYR D 40 PHE 0.018 0.001 PHE F 100 TRP 0.014 0.001 TRP M 137 HIS 0.011 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00368 (14874) covalent geometry : angle 0.67326 (21353) hydrogen bonds : bond 0.06008 ( 451) hydrogen bonds : angle 4.17881 ( 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 274 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8009 (tttt) cc_final: 0.7759 (ttpt) REVERT: A 63 ARG cc_start: 0.6833 (mmt-90) cc_final: 0.6122 (mmm-85) REVERT: A 92 LEU cc_start: 0.8112 (mt) cc_final: 0.7171 (tt) REVERT: A 125 ASP cc_start: 0.8052 (m-30) cc_final: 0.7819 (m-30) REVERT: B 27 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7701 (mm-40) REVERT: B 29 ILE cc_start: 0.8665 (mm) cc_final: 0.8345 (mm) REVERT: B 75 HIS cc_start: 0.8890 (t-90) cc_final: 0.8254 (t-170) REVERT: C 38 ASN cc_start: 0.7948 (m-40) cc_final: 0.7490 (p0) REVERT: C 41 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7340 (tt0) REVERT: C 74 LYS cc_start: 0.8716 (mttt) cc_final: 0.8487 (mmtp) REVERT: D 52 THR cc_start: 0.9161 (m) cc_final: 0.8617 (p) REVERT: D 82 HIS cc_start: 0.8249 (t-90) cc_final: 0.7979 (t-170) REVERT: D 86 ARG cc_start: 0.7061 (mpt-90) cc_final: 0.6258 (mtp180) REVERT: E 65 LEU cc_start: 0.8227 (tp) cc_final: 0.8003 (tt) REVERT: E 80 ARG cc_start: 0.8587 (pmt170) cc_final: 0.7705 (mmt90) REVERT: E 104 HIS cc_start: 0.8323 (t70) cc_final: 0.7765 (t70) REVERT: E 110 TYR cc_start: 0.8493 (t80) cc_final: 0.8209 (t80) REVERT: F 27 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8314 (mm-40) REVERT: F 92 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7416 (tmm-80) REVERT: G 20 ARG cc_start: 0.9316 (ttt180) cc_final: 0.8945 (tpt-90) REVERT: G 36 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7573 (tmtt) REVERT: G 38 ASN cc_start: 0.8925 (m-40) cc_final: 0.8356 (p0) REVERT: G 41 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7866 (tm-30) REVERT: G 85 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8146 (tt) REVERT: H 62 MET cc_start: 0.8567 (mmm) cc_final: 0.8179 (mmp) REVERT: H 71 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8178 (tm-30) REVERT: M 17 PRO cc_start: 0.7892 (Cg_exo) cc_final: 0.7630 (Cg_endo) REVERT: M 18 MET cc_start: 0.8933 (mmm) cc_final: 0.8726 (mmm) REVERT: M 50 GLN cc_start: 0.7895 (mt0) cc_final: 0.7692 (tt0) REVERT: M 51 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7725 (t-90) REVERT: M 74 MET cc_start: 0.8860 (tpp) cc_final: 0.8554 (tpt) REVERT: M 79 HIS cc_start: 0.8394 (p-80) cc_final: 0.7672 (m90) REVERT: M 133 ILE cc_start: 0.6357 (mt) cc_final: 0.6060 (tp) REVERT: M 135 ILE cc_start: 0.9036 (mp) cc_final: 0.8799 (mt) REVERT: M 137 TRP cc_start: 0.8644 (m100) cc_final: 0.8420 (m100) REVERT: M 151 TYR cc_start: 0.7708 (m-10) cc_final: 0.7444 (m-10) REVERT: M 162 PHE cc_start: 0.9077 (m-10) cc_final: 0.8773 (m-80) REVERT: M 171 ASN cc_start: 0.7808 (t0) cc_final: 0.7009 (t0) outliers start: 20 outliers final: 10 residues processed: 268 average time/residue: 0.1279 time to fit residues: 47.7685 Evaluate side-chains 215 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 41 VAL 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 85 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 524 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: 9.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS E 95 GLN E 104 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.084661 restraints weight = 24888.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087712 restraints weight = 12618.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089671 restraints weight = 8552.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090882 restraints weight = 6859.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091588 restraints weight = 6068.400| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 14874 Z= 0.382 Angle : 0.856 9.455 21353 Z= 0.477 Chirality : 0.047 0.226 2418 Planarity : 0.006 0.078 1677 Dihedral : 30.252 145.610 4410 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 8.19 % Allowed : 16.14 % Favored : 75.66 % 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: -3.74 (0.24), residues: 979 helix: -2.29 (0.19), residues: 569 sheet: -1.16 (0.86), residues: 28 loop : -2.69 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 526 TYR 0.053 0.003 TYR D 40 PHE 0.022 0.002 PHE B 100 TRP 0.013 0.003 TRP K 531 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00862 (14874) covalent geometry : angle 0.85641 (21353) hydrogen bonds : bond 0.06394 ( 451) hydrogen bonds : angle 4.89954 ( 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 280 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.379 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: 0.8325 (tttt) cc_final: 0.7953 (ttpt) REVERT: A 92 LEU cc_start: 0.8306 (mt) cc_final: 0.7494 (tt) REVERT: A 110 TYR cc_start: 0.8408 (t80) cc_final: 0.8106 (t80) REVERT: B 52 GLU cc_start: 0.8635 (tt0) cc_final: 0.8283 (tm-30) REVERT: C 38 ASN cc_start: 0.7958 (m-40) cc_final: 0.7691 (p0) REVERT: C 39 TYR cc_start: 0.8726 (m-80) cc_final: 0.8334 (m-80) REVERT: C 41 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7944 (tt0) REVERT: C 90 ASP cc_start: 0.8585 (t70) cc_final: 0.7883 (t0) REVERT: D 52 THR cc_start: 0.9210 (m) cc_final: 0.8701 (p) REVERT: D 86 ARG cc_start: 0.7662 (mpt-90) cc_final: 0.6817 (mtp180) REVERT: D 98 VAL cc_start: 0.9079 (t) cc_final: 0.8855 (p) REVERT: E 65 LEU cc_start: 0.8487 (tp) cc_final: 0.8236 (tt) REVERT: E 80 ARG cc_start: 0.8683 (pmt170) cc_final: 0.7715 (mmt90) REVERT: E 108 ASP cc_start: 0.9036 (t0) cc_final: 0.8782 (t70) REVERT: F 29 ILE cc_start: 0.8688 (mm) cc_final: 0.8397 (mm) REVERT: F 92 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: G 20 ARG cc_start: 0.9354 (ttt180) cc_final: 0.9076 (tpt-90) REVERT: G 36 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7698 (tmtt) REVERT: G 41 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8091 (tm-30) REVERT: H 59 MET cc_start: 0.7947 (tpp) cc_final: 0.7616 (tpp) REVERT: H 93 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7687 (mt-10) REVERT: M 3 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7970 (tm-30) REVERT: M 17 PRO cc_start: 0.8151 (Cg_exo) cc_final: 0.7897 (Cg_endo) REVERT: M 19 ASN cc_start: 0.9403 (t0) cc_final: 0.9131 (t0) REVERT: M 28 TRP cc_start: 0.7988 (t60) cc_final: 0.7786 (t60) REVERT: M 50 GLN cc_start: 0.8142 (mt0) cc_final: 0.7891 (mm-40) REVERT: M 74 MET cc_start: 0.8815 (tpp) cc_final: 0.8482 (tpt) REVERT: M 79 HIS cc_start: 0.8508 (p-80) cc_final: 0.7856 (m90) REVERT: M 151 TYR cc_start: 0.8199 (m-80) cc_final: 0.7740 (m-10) REVERT: M 162 PHE cc_start: 0.9108 (m-10) cc_final: 0.8866 (m-80) REVERT: M 171 ASN cc_start: 0.7673 (t0) cc_final: 0.6682 (t0) outliers start: 68 outliers final: 44 residues processed: 256 average time/residue: 0.1149 time to fit residues: 42.2288 Evaluate side-chains 239 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 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 A residue 113 THR 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 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ILE 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 119 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU 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 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 71 ILE 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: 2.9990 chunk 63 optimal weight: 0.0980 chunk 38 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3997 r_free = 0.3997 target = 0.148313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086246 restraints weight = 24566.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089428 restraints weight = 12441.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091519 restraints weight = 8441.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092686 restraints weight = 6773.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093470 restraints weight = 6025.239| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14874 Z= 0.241 Angle : 0.697 7.273 21353 Z= 0.400 Chirality : 0.040 0.195 2418 Planarity : 0.005 0.069 1677 Dihedral : 30.160 144.891 4410 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.78 % Allowed : 20.96 % Favored : 73.25 % 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: -3.17 (0.25), residues: 979 helix: -1.83 (0.20), residues: 574 sheet: -0.60 (0.91), residues: 28 loop : -2.48 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.046 0.002 TYR D 40 PHE 0.024 0.002 PHE B 100 TRP 0.017 0.002 TRP M 132 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00540 (14874) covalent geometry : angle 0.69725 (21353) hydrogen bonds : bond 0.05006 ( 451) hydrogen bonds : angle 4.15306 ( 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 255 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8289 (tttt) cc_final: 0.7845 (ttpt) REVERT: A 92 LEU cc_start: 0.8174 (mt) cc_final: 0.7436 (tt) REVERT: A 118 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7023 (mtt180) REVERT: B 40 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8393 (mmm-85) REVERT: B 52 GLU cc_start: 0.8536 (tt0) cc_final: 0.8202 (tm-30) REVERT: C 24 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8065 (mp10) REVERT: C 39 TYR cc_start: 0.8687 (m-80) cc_final: 0.8452 (m-80) REVERT: C 41 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7799 (tt0) REVERT: C 56 GLU cc_start: 0.7939 (tt0) cc_final: 0.7682 (tt0) REVERT: C 90 ASP cc_start: 0.8217 (t70) cc_final: 0.7530 (t0) REVERT: D 52 THR cc_start: 0.9188 (m) cc_final: 0.8650 (p) REVERT: D 86 ARG cc_start: 0.7438 (mpt-90) cc_final: 0.6592 (mtp180) REVERT: E 65 LEU cc_start: 0.8333 (tp) cc_final: 0.8068 (tt) REVERT: E 80 ARG cc_start: 0.8626 (pmt170) cc_final: 0.7624 (mmt90) REVERT: E 122 PHE cc_start: 0.7782 (m-80) cc_final: 0.7552 (m-80) REVERT: F 29 ILE cc_start: 0.8564 (mm) cc_final: 0.8266 (mm) REVERT: F 92 ARG cc_start: 0.8221 (tmm-80) cc_final: 0.7465 (tmm-80) REVERT: G 36 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7651 (tmtt) REVERT: G 38 ASN cc_start: 0.9046 (m-40) cc_final: 0.8746 (t0) REVERT: G 41 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8067 (tm-30) REVERT: G 99 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7057 (mtm180) REVERT: H 71 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8339 (tm-30) REVERT: H 93 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7723 (mt-10) REVERT: L 530 TRP cc_start: 0.8216 (p-90) cc_final: 0.7903 (p-90) REVERT: M 17 PRO cc_start: 0.8174 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: M 19 ASN cc_start: 0.9370 (t0) cc_final: 0.9108 (t0) REVERT: M 28 TRP cc_start: 0.8064 (t60) cc_final: 0.7803 (t60) REVERT: M 74 MET cc_start: 0.8847 (tpp) cc_final: 0.8328 (tpt) REVERT: M 79 HIS cc_start: 0.8407 (p-80) cc_final: 0.7781 (m90) REVERT: M 162 PHE cc_start: 0.9077 (m-10) cc_final: 0.8738 (m-80) REVERT: M 171 ASN cc_start: 0.7500 (t0) cc_final: 0.6533 (t0) outliers start: 48 outliers final: 38 residues processed: 233 average time/residue: 0.1259 time to fit residues: 40.8722 Evaluate side-chains 233 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 113 THR Chi-restraints excluded: chain A residue 118 ARG 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 93 GLN 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 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 41 VAL 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 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 25 ASN C 84 GLN D 82 HIS E 45 GLN E 59 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.148630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086351 restraints weight = 24577.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089504 restraints weight = 12451.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091592 restraints weight = 8450.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.092862 restraints weight = 6767.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093598 restraints weight = 5981.548| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14874 Z= 0.236 Angle : 0.690 8.936 21353 Z= 0.395 Chirality : 0.040 0.188 2418 Planarity : 0.005 0.069 1677 Dihedral : 30.022 140.922 4410 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 6.51 % Allowed : 22.29 % Favored : 71.20 % 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: -2.87 (0.25), residues: 979 helix: -1.61 (0.20), residues: 572 sheet: -0.40 (0.95), residues: 28 loop : -2.33 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.022 0.002 TYR F 88 PHE 0.020 0.001 PHE B 100 TRP 0.015 0.002 TRP M 132 HIS 0.014 0.002 HIS M 185 Details of bonding type rmsd covalent geometry : bond 0.00526 (14874) covalent geometry : angle 0.68987 (21353) hydrogen bonds : bond 0.04903 ( 451) hydrogen bonds : angle 4.07771 ( 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 252 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8206 (tttt) cc_final: 0.7813 (ttpt) REVERT: A 92 LEU cc_start: 0.8145 (mt) cc_final: 0.7423 (tt) REVERT: A 110 TYR cc_start: 0.8318 (t80) cc_final: 0.8011 (t80) REVERT: B 25 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7345 (t0) REVERT: B 75 HIS cc_start: 0.8668 (t70) cc_final: 0.8463 (t-170) REVERT: C 24 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8033 (mp10) REVERT: C 39 TYR cc_start: 0.8500 (m-80) cc_final: 0.8233 (m-80) REVERT: C 41 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7881 (tt0) REVERT: C 56 GLU cc_start: 0.8058 (tt0) cc_final: 0.7700 (tt0) REVERT: C 90 ASP cc_start: 0.8122 (t70) cc_final: 0.7579 (t0) REVERT: D 52 THR cc_start: 0.9232 (m) cc_final: 0.8748 (p) REVERT: D 86 ARG cc_start: 0.7485 (mpt-90) cc_final: 0.6654 (mtp180) REVERT: D 98 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8793 (p) REVERT: E 65 LEU cc_start: 0.8374 (tp) cc_final: 0.8162 (tt) REVERT: E 80 ARG cc_start: 0.8622 (pmt170) cc_final: 0.7664 (mmt90) REVERT: F 29 ILE cc_start: 0.8622 (mm) cc_final: 0.8311 (mm) REVERT: F 92 ARG cc_start: 0.8214 (tmm-80) cc_final: 0.7404 (tmm-80) REVERT: G 36 LYS cc_start: 0.8104 (mmpt) cc_final: 0.7557 (tmtt) REVERT: G 41 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8084 (tm-30) REVERT: H 71 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 93 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7905 (mt-10) REVERT: K 523 ILE cc_start: 0.8674 (mp) cc_final: 0.8416 (pt) REVERT: M 3 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7941 (tm-30) REVERT: M 17 PRO cc_start: 0.8146 (Cg_exo) cc_final: 0.7869 (Cg_endo) REVERT: M 19 ASN cc_start: 0.9317 (t0) cc_final: 0.9052 (t0) REVERT: M 28 TRP cc_start: 0.8076 (t60) cc_final: 0.7802 (t60) REVERT: M 74 MET cc_start: 0.8799 (tpp) cc_final: 0.8509 (tpp) REVERT: M 79 HIS cc_start: 0.8372 (p-80) cc_final: 0.7968 (m90) REVERT: M 101 MET cc_start: 0.6967 (ptp) cc_final: 0.6628 (mpp) REVERT: M 162 PHE cc_start: 0.9081 (m-10) cc_final: 0.8802 (m-80) REVERT: M 171 ASN cc_start: 0.7678 (t0) cc_final: 0.6806 (t0) outliers start: 54 outliers final: 45 residues processed: 226 average time/residue: 0.1165 time to fit residues: 37.3667 Evaluate side-chains 236 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 25 ASN 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 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 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ILE 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 57 SER Chi-restraints excluded: chain E residue 95 GLN 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 G residue 16 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 71 ILE 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: 6.9990 chunk 119 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 82 HIS E 59 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3977 r_free = 0.3977 target = 0.146055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084253 restraints weight = 24434.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087283 restraints weight = 12611.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089232 restraints weight = 8642.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090418 restraints weight = 6972.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091066 restraints weight = 6193.604| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14874 Z= 0.272 Angle : 0.717 9.609 21353 Z= 0.406 Chirality : 0.041 0.177 2418 Planarity : 0.005 0.068 1677 Dihedral : 30.040 137.192 4410 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 7.35 % Allowed : 22.29 % Favored : 70.36 % 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: -2.74 (0.26), residues: 979 helix: -1.50 (0.21), residues: 569 sheet: -0.30 (0.96), residues: 28 loop : -2.29 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.026 0.002 TYR F 98 PHE 0.018 0.002 PHE B 100 TRP 0.015 0.002 TRP M 132 HIS 0.011 0.002 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00609 (14874) covalent geometry : angle 0.71738 (21353) hydrogen bonds : bond 0.04995 ( 451) hydrogen bonds : angle 4.22388 ( 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 253 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8307 (tttt) cc_final: 0.7897 (ttpt) REVERT: A 92 LEU cc_start: 0.8209 (mt) cc_final: 0.7498 (tt) REVERT: A 107 GLU cc_start: 0.8387 (tt0) cc_final: 0.7945 (tm-30) REVERT: A 114 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 118 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7298 (mtt180) REVERT: C 39 TYR cc_start: 0.8510 (m-80) cc_final: 0.8194 (m-80) REVERT: C 41 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7878 (tt0) REVERT: C 90 ASP cc_start: 0.8179 (t70) cc_final: 0.7647 (t0) REVERT: D 52 THR cc_start: 0.9200 (m) cc_final: 0.8710 (p) REVERT: D 86 ARG cc_start: 0.7543 (mpt-90) cc_final: 0.6709 (mtp180) REVERT: D 98 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (p) REVERT: E 65 LEU cc_start: 0.8451 (tp) cc_final: 0.8219 (tt) REVERT: E 80 ARG cc_start: 0.8601 (pmt170) cc_final: 0.7656 (mmt90) REVERT: E 118 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7779 (mtt90) REVERT: F 29 ILE cc_start: 0.8613 (mm) cc_final: 0.8265 (mm) REVERT: F 92 ARG cc_start: 0.8252 (tmm-80) cc_final: 0.7417 (tmm-80) REVERT: F 100 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: G 36 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7574 (tmtt) REVERT: G 41 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8034 (tm-30) REVERT: G 99 ARG cc_start: 0.8511 (mmt90) cc_final: 0.7514 (mtm180) REVERT: H 35 GLU cc_start: 0.7338 (mp0) cc_final: 0.7082 (mp0) REVERT: H 71 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 93 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7979 (mt-10) REVERT: L 530 TRP cc_start: 0.8163 (p-90) cc_final: 0.7858 (p-90) REVERT: M 17 PRO cc_start: 0.8126 (Cg_exo) cc_final: 0.7843 (Cg_endo) REVERT: M 18 MET cc_start: 0.8472 (mmm) cc_final: 0.8259 (mmm) REVERT: M 19 ASN cc_start: 0.9306 (t0) cc_final: 0.9037 (t0) REVERT: M 28 TRP cc_start: 0.8116 (t60) cc_final: 0.7855 (t60) REVERT: M 74 MET cc_start: 0.8787 (tpp) cc_final: 0.8289 (tpt) REVERT: M 79 HIS cc_start: 0.8469 (p-80) cc_final: 0.7958 (m90) REVERT: M 101 MET cc_start: 0.7000 (ptp) cc_final: 0.6670 (mpp) REVERT: M 162 PHE cc_start: 0.9017 (m-10) cc_final: 0.8734 (m-80) REVERT: M 171 ASN cc_start: 0.7782 (t0) cc_final: 0.6874 (t0) outliers start: 61 outliers final: 52 residues processed: 226 average time/residue: 0.1185 time to fit residues: 38.4318 Evaluate side-chains 245 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 THR 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 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ILE 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 57 SER Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 127 GLN 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 100 PHE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 533 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 172 THR 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: 5.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS ** H 84 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 = 0.4070 r_free = 0.4070 target = 0.154716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092001 restraints weight = 24119.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095519 restraints weight = 11845.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097834 restraints weight = 7902.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099200 restraints weight = 6275.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100062 restraints weight = 5537.689| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14874 Z= 0.150 Angle : 0.616 11.599 21353 Z= 0.357 Chirality : 0.036 0.154 2418 Planarity : 0.004 0.057 1677 Dihedral : 29.862 140.592 4410 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.37 % Allowed : 26.02 % Favored : 70.60 % 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: -2.30 (0.26), residues: 979 helix: -1.03 (0.21), residues: 576 sheet: -0.17 (0.95), residues: 28 loop : -2.31 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.021 0.002 TYR A 110 PHE 0.021 0.001 PHE B 100 TRP 0.015 0.001 TRP L 530 HIS 0.011 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00319 (14874) covalent geometry : angle 0.61634 (21353) hydrogen bonds : bond 0.04154 ( 451) hydrogen bonds : angle 3.42056 ( 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 235 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6332 (mmp80) cc_final: 0.5301 (mmm-85) REVERT: B 29 ILE cc_start: 0.8547 (mm) cc_final: 0.8212 (mm) REVERT: C 41 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7441 (tt0) REVERT: C 71 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8104 (ttm-80) REVERT: D 37 TYR cc_start: 0.8603 (m-80) cc_final: 0.8340 (m-80) REVERT: D 86 ARG cc_start: 0.7084 (mpt-90) cc_final: 0.6247 (mtp180) REVERT: E 80 ARG cc_start: 0.8574 (pmt170) cc_final: 0.7497 (mmt90) REVERT: E 95 GLN cc_start: 0.8798 (tp40) cc_final: 0.8597 (mm-40) REVERT: F 44 LYS cc_start: 0.8000 (tptt) cc_final: 0.7501 (tptt) REVERT: F 47 SER cc_start: 0.8925 (t) cc_final: 0.8225 (m) REVERT: G 36 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7466 (tmtt) REVERT: G 38 ASN cc_start: 0.9002 (m-40) cc_final: 0.8732 (p0) REVERT: G 41 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7911 (tm-30) REVERT: G 63 LEU cc_start: 0.7610 (mt) cc_final: 0.7128 (tp) REVERT: G 99 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8275 (mmt90) REVERT: H 71 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8252 (tm-30) REVERT: H 93 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8013 (mt-10) REVERT: H 105 GLU cc_start: 0.8330 (tp30) cc_final: 0.8111 (tp30) REVERT: M 17 PRO cc_start: 0.7882 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: M 18 MET cc_start: 0.8320 (mmm) cc_final: 0.8044 (mmm) REVERT: M 19 ASN cc_start: 0.9306 (t0) cc_final: 0.9085 (t0) REVERT: M 79 HIS cc_start: 0.8347 (p-80) cc_final: 0.7879 (m90) REVERT: M 101 MET cc_start: 0.6950 (ptp) cc_final: 0.6682 (ptp) REVERT: M 131 VAL cc_start: 0.7824 (p) cc_final: 0.7538 (m) REVERT: M 171 ASN cc_start: 0.7740 (t0) cc_final: 0.6859 (t0) outliers start: 28 outliers final: 17 residues processed: 224 average time/residue: 0.1212 time to fit residues: 38.2851 Evaluate side-chains 202 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092219 restraints weight = 23743.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095645 restraints weight = 11681.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097899 restraints weight = 7801.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099246 restraints weight = 6194.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100067 restraints weight = 5464.102| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14874 Z= 0.149 Angle : 0.612 10.738 21353 Z= 0.351 Chirality : 0.036 0.153 2418 Planarity : 0.004 0.048 1677 Dihedral : 29.765 138.642 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.17 % Allowed : 28.67 % Favored : 69.16 % 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: -0.65 (0.22), residues: 569 sheet: 0.18 (1.00), residues: 26 loop : -2.12 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 52 TYR 0.021 0.002 TYR H 83 PHE 0.025 0.001 PHE B 100 TRP 0.034 0.002 TRP M 28 HIS 0.007 0.001 HIS M 185 Details of bonding type rmsd covalent geometry : bond 0.00322 (14874) covalent geometry : angle 0.61185 (21353) hydrogen bonds : bond 0.03927 ( 451) hydrogen bonds : angle 3.32061 ( 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 223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8223 (tt0) cc_final: 0.7864 (tm-30) REVERT: A 139 LEU cc_start: 0.7708 (tt) cc_final: 0.7328 (tt) REVERT: B 29 ILE cc_start: 0.8520 (mm) cc_final: 0.7880 (mm) REVERT: C 24 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8484 (mp10) REVERT: C 41 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7607 (tt0) REVERT: C 56 GLU cc_start: 0.7974 (tt0) cc_final: 0.6994 (tt0) REVERT: C 71 ARG cc_start: 0.8480 (mtm110) cc_final: 0.8031 (ttm-80) REVERT: D 37 TYR cc_start: 0.8618 (m-80) cc_final: 0.8372 (m-80) REVERT: D 52 THR cc_start: 0.9201 (m) cc_final: 0.8688 (p) REVERT: D 86 ARG cc_start: 0.7110 (mpt-90) cc_final: 0.6252 (mtp180) REVERT: E 65 LEU cc_start: 0.8296 (tp) cc_final: 0.8049 (tt) REVERT: E 80 ARG cc_start: 0.8507 (pmt170) cc_final: 0.7505 (mmt90) REVERT: E 95 GLN cc_start: 0.8849 (tp40) cc_final: 0.8632 (mm-40) REVERT: F 44 LYS cc_start: 0.7957 (tptt) cc_final: 0.7728 (tptm) REVERT: F 47 SER cc_start: 0.8868 (t) cc_final: 0.8227 (m) REVERT: F 92 ARG cc_start: 0.8218 (tmm-80) cc_final: 0.7709 (tmm-80) REVERT: G 36 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7525 (tmtt) REVERT: G 38 ASN cc_start: 0.9025 (m-40) cc_final: 0.8812 (p0) REVERT: G 41 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7930 (tm-30) REVERT: H 71 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8237 (tm-30) REVERT: H 93 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8008 (mt-10) REVERT: M 17 PRO cc_start: 0.7744 (Cg_exo) cc_final: 0.7381 (Cg_endo) REVERT: M 18 MET cc_start: 0.8324 (mmm) cc_final: 0.8054 (mmm) REVERT: M 19 ASN cc_start: 0.9354 (t0) cc_final: 0.9123 (t0) REVERT: M 28 TRP cc_start: 0.8100 (t60) cc_final: 0.7775 (t-100) REVERT: M 79 HIS cc_start: 0.8436 (p-80) cc_final: 0.7694 (m90) REVERT: M 101 MET cc_start: 0.6614 (ptp) cc_final: 0.6365 (mpp) REVERT: M 171 ASN cc_start: 0.7896 (t0) cc_final: 0.7063 (t0) outliers start: 18 outliers final: 16 residues processed: 216 average time/residue: 0.1061 time to fit residues: 33.5206 Evaluate side-chains 209 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 23 LEU 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 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093375 restraints weight = 23703.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096843 restraints weight = 11669.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099078 restraints weight = 7790.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100498 restraints weight = 6207.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101319 restraints weight = 5465.010| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14874 Z= 0.147 Angle : 0.619 14.670 21353 Z= 0.349 Chirality : 0.036 0.153 2418 Planarity : 0.004 0.042 1677 Dihedral : 29.713 139.587 4410 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.65 % Allowed : 28.67 % Favored : 68.67 % 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: -1.62 (0.27), residues: 979 helix: -0.47 (0.22), residues: 571 sheet: 0.44 (1.03), residues: 26 loop : -2.05 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 131 TYR 0.027 0.002 TYR A 110 PHE 0.019 0.001 PHE B 100 TRP 0.043 0.002 TRP L 531 HIS 0.012 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00317 (14874) covalent geometry : angle 0.61916 (21353) hydrogen bonds : bond 0.03885 ( 451) hydrogen bonds : angle 3.24286 ( 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 217 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6416 (mmp80) cc_final: 0.4943 (mmm-85) REVERT: A 131 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7193 (ttp80) REVERT: C 24 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8111 (mp10) REVERT: C 41 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7539 (tt0) REVERT: C 71 ARG cc_start: 0.8514 (mtm110) cc_final: 0.8091 (ttm-80) REVERT: D 37 TYR cc_start: 0.8605 (m-80) cc_final: 0.8351 (m-80) REVERT: D 86 ARG cc_start: 0.7068 (mpt-90) cc_final: 0.6097 (mtp180) REVERT: E 80 ARG cc_start: 0.8547 (pmt170) cc_final: 0.7444 (mmt90) REVERT: E 95 GLN cc_start: 0.8834 (tp40) cc_final: 0.8596 (mm-40) REVERT: E 96 GLU cc_start: 0.9135 (tp30) cc_final: 0.8668 (mm-30) REVERT: E 122 PHE cc_start: 0.7499 (m-80) cc_final: 0.7278 (m-80) REVERT: F 44 LYS cc_start: 0.7860 (tptt) cc_final: 0.7581 (tptm) REVERT: F 47 SER cc_start: 0.8838 (t) cc_final: 0.8174 (m) REVERT: F 92 ARG cc_start: 0.8173 (tmm-80) cc_final: 0.7643 (tmm-80) REVERT: G 36 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7472 (tmtt) REVERT: G 41 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7845 (tm-30) REVERT: G 85 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7960 (tt) REVERT: H 35 GLU cc_start: 0.7083 (mp0) cc_final: 0.6861 (mp0) REVERT: H 71 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8200 (tm-30) REVERT: L 531 TRP cc_start: 0.8855 (p90) cc_final: 0.8606 (p90) REVERT: M 18 MET cc_start: 0.8279 (mmm) cc_final: 0.8038 (mmm) REVERT: M 19 ASN cc_start: 0.9354 (t0) cc_final: 0.9138 (t0) REVERT: M 28 TRP cc_start: 0.8054 (t60) cc_final: 0.7723 (t-100) REVERT: M 79 HIS cc_start: 0.8430 (p-80) cc_final: 0.7713 (m90) REVERT: M 101 MET cc_start: 0.6654 (ptp) cc_final: 0.6196 (pmm) REVERT: M 131 VAL cc_start: 0.7876 (p) cc_final: 0.7601 (m) REVERT: M 171 ASN cc_start: 0.7893 (t0) cc_final: 0.7026 (t0) outliers start: 22 outliers final: 17 residues processed: 210 average time/residue: 0.1070 time to fit residues: 33.2090 Evaluate side-chains 202 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 23 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 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE 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: 8.9990 chunk 96 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.180902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.109382 restraints weight = 22666.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.112935 restraints weight = 11288.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115231 restraints weight = 7659.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116578 restraints weight = 6188.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117360 restraints weight = 5527.169| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.195 Angle : 0.657 13.337 21353 Z= 0.367 Chirality : 0.038 0.148 2418 Planarity : 0.004 0.047 1677 Dihedral : 29.720 135.888 4410 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.65 % Allowed : 29.16 % Favored : 68.19 % 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: -1.67 (0.27), residues: 979 helix: -0.48 (0.22), residues: 571 sheet: -0.33 (0.99), residues: 31 loop : -2.09 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 521 TYR 0.029 0.002 TYR A 110 PHE 0.028 0.002 PHE B 100 TRP 0.049 0.003 TRP L 531 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00435 (14874) covalent geometry : angle 0.65737 (21353) hydrogen bonds : bond 0.04264 ( 451) hydrogen bonds : angle 3.55793 ( 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 208 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7603 (tt0) REVERT: C 56 GLU cc_start: 0.8109 (tt0) cc_final: 0.7155 (tt0) REVERT: C 71 ARG cc_start: 0.8531 (mtm110) cc_final: 0.8091 (ttm-80) REVERT: C 75 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7377 (mttt) REVERT: D 37 TYR cc_start: 0.8821 (m-80) cc_final: 0.8427 (m-80) REVERT: D 82 HIS cc_start: 0.8119 (t70) cc_final: 0.7855 (t-170) REVERT: D 86 ARG cc_start: 0.7317 (mpt-90) cc_final: 0.6489 (mtp180) REVERT: E 65 LEU cc_start: 0.8401 (tp) cc_final: 0.8161 (tt) REVERT: E 80 ARG cc_start: 0.8555 (pmt170) cc_final: 0.7608 (mmt90) REVERT: F 29 ILE cc_start: 0.8089 (mm) cc_final: 0.7885 (mm) REVERT: F 44 LYS cc_start: 0.7906 (tptt) cc_final: 0.7620 (tptm) REVERT: F 47 SER cc_start: 0.9087 (t) cc_final: 0.8347 (m) REVERT: G 36 LYS cc_start: 0.8095 (mmpt) cc_final: 0.7637 (tmtt) REVERT: G 41 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 85 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8213 (tt) REVERT: H 35 GLU cc_start: 0.7211 (mp0) cc_final: 0.6960 (mp0) REVERT: H 71 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8164 (tm-30) REVERT: L 531 TRP cc_start: 0.8885 (p90) cc_final: 0.8520 (p90) REVERT: M 19 ASN cc_start: 0.9332 (t0) cc_final: 0.9098 (t0) REVERT: M 28 TRP cc_start: 0.8150 (t60) cc_final: 0.7767 (t-100) REVERT: M 79 HIS cc_start: 0.8445 (p-80) cc_final: 0.7714 (m90) REVERT: M 171 ASN cc_start: 0.7950 (t0) cc_final: 0.7098 (t0) outliers start: 22 outliers final: 20 residues processed: 200 average time/residue: 0.1091 time to fit residues: 31.7506 Evaluate side-chains 201 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 23 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 122 THR Chi-restraints excluded: chain E residue 57 SER 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 19 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE 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: 5.9990 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN E 127 GLN ** F 93 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.153086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090580 restraints weight = 23917.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093913 restraints weight = 12171.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096114 restraints weight = 8255.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097408 restraints weight = 6609.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098253 restraints weight = 5847.456| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14874 Z= 0.168 Angle : 0.631 12.590 21353 Z= 0.355 Chirality : 0.037 0.151 2418 Planarity : 0.004 0.052 1677 Dihedral : 29.704 137.532 4410 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.77 % Allowed : 28.31 % Favored : 68.92 % 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: -1.49 (0.27), residues: 979 helix: -0.33 (0.22), residues: 571 sheet: 0.80 (1.04), residues: 26 loop : -2.07 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 521 TYR 0.027 0.002 TYR A 110 PHE 0.023 0.001 PHE B 100 TRP 0.034 0.002 TRP L 531 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00370 (14874) covalent geometry : angle 0.63121 (21353) hydrogen bonds : bond 0.04084 ( 451) hydrogen bonds : angle 3.44689 ( 1181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.20 seconds wall clock time: 41 minutes 24.11 seconds (2484.11 seconds total)