Starting phenix.real_space_refine on Thu Jul 31 16:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6muo_9250/07_2025/6muo_9250_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6muo_9250/07_2025/6muo_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_9250/07_2025/6muo_9250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6muo_9250/07_2025/6muo_9250.map" model { file = "/net/cci-nas-00/data/ceres_data/6muo_9250/07_2025/6muo_9250_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6muo_9250/07_2025/6muo_9250_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.61, per 1000 atoms: 0.61 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: 3.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.30 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: 5.01 Time building geometry restraints manager: 4.01 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: 0.520 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP K 531 HIS 0.011 0.002 HIS F 75 PHE 0.019 0.003 PHE A 84 TYR 0.024 0.003 TYR F 98 ARG 0.006 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.31499 ( 451) hydrogen bonds : angle 11.35678 ( 1181) covalent geometry : bond 0.00754 (14874) covalent geometry : angle 0.95289 (21353) *********************** 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 : 1.054 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: 0.8267 (m-80) REVERT: C 41 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7403 (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: 0.6978 (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: 0.7880 (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: 0.7593 (tttm) REVERT: G 38 ASN cc_start: 0.8894 (m-40) cc_final: 0.8082 (p0) REVERT: G 41 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7988 (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: 0.7589 (tm-30) REVERT: H 93 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8029 (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: 0.7752 (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: 0.3501 time to fit residues: 161.3545 Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 103 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.0050 chunk 111 optimal weight: 30.0000 overall best weight: 1.7598 ------------------------------------------------------------------------------- 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.090691 restraints weight = 24132.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094229 restraints weight = 11667.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096535 restraints weight = 7698.889| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14874 Z= 0.195 Angle : 0.696 8.838 21353 Z= 0.406 Chirality : 0.041 0.269 2418 Planarity : 0.005 0.037 1677 Dihedral : 30.242 160.131 4415 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.89 % Allowed : 13.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.21), residues: 979 helix: -2.99 (0.16), residues: 572 sheet: -1.45 (0.86), residues: 28 loop : -2.79 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 28 HIS 0.012 0.001 HIS D 82 PHE 0.018 0.002 PHE F 100 TYR 0.025 0.002 TYR D 40 ARG 0.015 0.001 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 451) hydrogen bonds : angle 4.31966 ( 1181) covalent geometry : bond 0.00425 (14874) covalent geometry : angle 0.69643 (21353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 1.085 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: 0.8043 (tttt) cc_final: 0.7702 (ttpt) REVERT: A 63 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6151 (mmm-85) REVERT: A 92 LEU cc_start: 0.8101 (mt) cc_final: 0.7275 (tt) REVERT: A 125 ASP cc_start: 0.8227 (m-30) cc_final: 0.8000 (m-30) REVERT: B 27 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7745 (mm-40) REVERT: B 29 ILE cc_start: 0.8738 (mm) cc_final: 0.8414 (mm) REVERT: B 40 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8356 (mmm-85) REVERT: B 75 HIS cc_start: 0.8946 (t-90) cc_final: 0.8632 (t-170) REVERT: C 38 ASN cc_start: 0.7885 (m-40) cc_final: 0.7454 (p0) REVERT: C 39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8559 (m-80) REVERT: C 41 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7401 (tt0) REVERT: D 52 THR cc_start: 0.9214 (m) cc_final: 0.8680 (p) REVERT: D 62 MET cc_start: 0.9178 (tpp) cc_final: 0.8727 (mmp) REVERT: D 82 HIS cc_start: 0.8273 (t-90) cc_final: 0.7999 (t-170) REVERT: D 86 ARG cc_start: 0.7116 (mpt-90) cc_final: 0.6318 (mtp180) REVERT: E 65 LEU cc_start: 0.8264 (tp) cc_final: 0.8028 (tt) REVERT: E 80 ARG cc_start: 0.8663 (pmt170) cc_final: 0.7704 (mmt90) REVERT: E 104 HIS cc_start: 0.8339 (t70) cc_final: 0.7782 (t70) REVERT: E 110 TYR cc_start: 0.8550 (t80) cc_final: 0.8312 (t80) REVERT: E 136 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8320 (mm-30) REVERT: F 92 ARG cc_start: 0.8052 (tmm-80) cc_final: 0.7545 (tmm-80) REVERT: G 20 ARG cc_start: 0.9322 (ttt180) cc_final: 0.8962 (tpt-90) REVERT: G 36 LYS cc_start: 0.8084 (mmpt) cc_final: 0.7593 (tmtt) REVERT: G 38 ASN cc_start: 0.8965 (m-40) cc_final: 0.8367 (p0) REVERT: G 41 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7873 (tm-30) REVERT: H 62 MET cc_start: 0.8554 (mmm) cc_final: 0.8142 (mmp) REVERT: H 71 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8194 (tm-30) REVERT: H 93 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7863 (mt-10) REVERT: M 17 PRO cc_start: 0.7968 (Cg_exo) cc_final: 0.7726 (Cg_endo) REVERT: M 18 MET cc_start: 0.8902 (mmm) cc_final: 0.8676 (mmm) REVERT: M 50 GLN cc_start: 0.7917 (mt0) cc_final: 0.7667 (tt0) REVERT: M 51 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7809 (t-90) REVERT: M 74 MET cc_start: 0.8861 (tpp) cc_final: 0.8564 (tpt) REVERT: M 79 HIS cc_start: 0.8447 (p-80) cc_final: 0.7761 (m90) REVERT: M 133 ILE cc_start: 0.6021 (mt) cc_final: 0.5761 (tp) REVERT: M 135 ILE cc_start: 0.9023 (mp) cc_final: 0.8752 (mt) REVERT: M 137 TRP cc_start: 0.8618 (m100) cc_final: 0.8323 (m100) REVERT: M 151 TYR cc_start: 0.7672 (m-10) cc_final: 0.7376 (m-10) REVERT: M 162 PHE cc_start: 0.9105 (m-10) cc_final: 0.8726 (m-80) REVERT: M 171 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6727 (t0) outliers start: 24 outliers final: 12 residues processed: 260 average time/residue: 0.2867 time to fit residues: 104.0761 Evaluate side-chains 222 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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 49 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 49 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 171 ASN 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 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 93 GLN C 82 HIS C 84 GLN E 59 HIS E 95 GLN E 104 HIS F 93 GLN H 47 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.090597 restraints weight = 24232.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094064 restraints weight = 11897.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096324 restraints weight = 7939.166| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14874 Z= 0.184 Angle : 0.648 7.595 21353 Z= 0.378 Chirality : 0.038 0.187 2418 Planarity : 0.005 0.061 1677 Dihedral : 30.031 147.750 4410 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.42 % Allowed : 17.35 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.24), residues: 979 helix: -1.94 (0.19), residues: 564 sheet: -0.99 (0.89), residues: 28 loop : -2.39 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 530 HIS 0.005 0.001 HIS B 75 PHE 0.018 0.001 PHE B 100 TYR 0.040 0.002 TYR D 40 ARG 0.007 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 451) hydrogen bonds : angle 3.74325 ( 1181) covalent geometry : bond 0.00404 (14874) covalent geometry : angle 0.64752 (21353) *********************** 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 266 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6637 (mmt-90) cc_final: 0.5895 (mmm-85) REVERT: A 95 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: B 29 ILE cc_start: 0.8731 (mm) cc_final: 0.8377 (mm) REVERT: B 40 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8473 (mmm-85) REVERT: B 75 HIS cc_start: 0.8987 (t-90) cc_final: 0.8608 (t-170) REVERT: C 38 ASN cc_start: 0.7804 (m-40) cc_final: 0.7464 (p0) REVERT: C 39 TYR cc_start: 0.8835 (m-80) cc_final: 0.8594 (m-80) REVERT: C 41 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7493 (tt0) REVERT: D 52 THR cc_start: 0.9117 (m) cc_final: 0.8445 (p) REVERT: D 86 ARG cc_start: 0.7166 (mpt-90) cc_final: 0.6311 (mtp180) REVERT: E 80 ARG cc_start: 0.8598 (pmt170) cc_final: 0.7615 (mmt90) REVERT: E 95 GLN cc_start: 0.8270 (tt0) cc_final: 0.7832 (tp40) REVERT: E 96 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8455 (mm-30) REVERT: E 104 HIS cc_start: 0.8304 (t-90) cc_final: 0.7864 (t70) REVERT: F 29 ILE cc_start: 0.8627 (mm) cc_final: 0.8340 (mm) REVERT: F 92 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7496 (tmm-80) REVERT: G 20 ARG cc_start: 0.9298 (ttt180) cc_final: 0.8970 (tpt-90) REVERT: G 36 LYS cc_start: 0.8102 (mmpt) cc_final: 0.7630 (tmtt) REVERT: G 38 ASN cc_start: 0.8909 (m-40) cc_final: 0.8413 (p0) REVERT: G 41 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7903 (tm-30) REVERT: G 51 LEU cc_start: 0.8160 (tp) cc_final: 0.7840 (tt) REVERT: G 56 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7641 (tm-30) REVERT: H 71 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8173 (tm-30) REVERT: H 93 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7825 (mt-10) REVERT: H 105 GLU cc_start: 0.8356 (tp30) cc_final: 0.8148 (tp30) REVERT: M 17 PRO cc_start: 0.7977 (Cg_exo) cc_final: 0.7691 (Cg_endo) REVERT: M 18 MET cc_start: 0.8811 (mmm) cc_final: 0.8531 (mmm) REVERT: M 19 ASN cc_start: 0.9340 (t0) cc_final: 0.9128 (t0) REVERT: M 28 TRP cc_start: 0.7916 (t60) cc_final: 0.7567 (t60) REVERT: M 51 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7805 (t-90) REVERT: M 74 MET cc_start: 0.8850 (tpp) cc_final: 0.8548 (tpt) REVERT: M 79 HIS cc_start: 0.8348 (p-80) cc_final: 0.7711 (m90) REVERT: M 135 ILE cc_start: 0.8908 (mp) cc_final: 0.8616 (mt) REVERT: M 137 TRP cc_start: 0.8522 (m100) cc_final: 0.8173 (m100) REVERT: M 171 ASN cc_start: 0.7492 (t160) cc_final: 0.6879 (t0) outliers start: 45 outliers final: 26 residues processed: 244 average time/residue: 0.2851 time to fit residues: 98.5815 Evaluate side-chains 221 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU 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 100 VAL 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 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 F residue 60 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 51 HIS 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 31 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 114 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 93 GLN D 82 HIS F 93 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092885 restraints weight = 23911.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096456 restraints weight = 11679.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098738 restraints weight = 7776.219| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14874 Z= 0.153 Angle : 0.603 7.875 21353 Z= 0.353 Chirality : 0.036 0.186 2418 Planarity : 0.004 0.055 1677 Dihedral : 29.889 145.190 4410 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.46 % Allowed : 18.31 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.26), residues: 979 helix: -1.41 (0.21), residues: 570 sheet: -0.29 (0.96), residues: 26 loop : -2.19 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 530 HIS 0.010 0.001 HIS D 82 PHE 0.018 0.001 PHE B 100 TYR 0.023 0.002 TYR D 40 ARG 0.006 0.000 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 451) hydrogen bonds : angle 3.39834 ( 1181) covalent geometry : bond 0.00331 (14874) covalent geometry : angle 0.60295 (21353) *********************** 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 244 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7125 (ptp-170) REVERT: B 29 ILE cc_start: 0.8595 (mm) cc_final: 0.8279 (mm) REVERT: C 24 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8143 (mp10) REVERT: C 38 ASN cc_start: 0.7887 (m-40) cc_final: 0.7628 (p0) REVERT: C 39 TYR cc_start: 0.8787 (m-80) cc_final: 0.8575 (m-80) REVERT: C 41 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7556 (tt0) REVERT: C 56 GLU cc_start: 0.7809 (tt0) cc_final: 0.6848 (tt0) REVERT: D 59 MET cc_start: 0.8193 (tpp) cc_final: 0.7969 (tpp) REVERT: D 86 ARG cc_start: 0.6993 (mpt-90) cc_final: 0.6095 (mtp180) REVERT: E 80 ARG cc_start: 0.8503 (pmt170) cc_final: 0.7428 (mmt90) REVERT: E 95 GLN cc_start: 0.8198 (tt0) cc_final: 0.7852 (mm-40) REVERT: F 29 ILE cc_start: 0.8535 (mm) cc_final: 0.8163 (mm) REVERT: F 92 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7298 (tmm-80) REVERT: F 93 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: F 97 LEU cc_start: 0.8367 (tp) cc_final: 0.8109 (tp) REVERT: F 98 TYR cc_start: 0.8363 (m-80) cc_final: 0.7974 (m-80) REVERT: G 20 ARG cc_start: 0.9257 (ttt180) cc_final: 0.8915 (tpt-90) REVERT: G 36 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7577 (tmtt) REVERT: G 38 ASN cc_start: 0.8878 (m-40) cc_final: 0.8591 (p0) REVERT: G 41 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 51 LEU cc_start: 0.7987 (tp) cc_final: 0.7760 (tt) REVERT: G 56 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7596 (tm-30) REVERT: G 85 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8254 (tt) REVERT: H 71 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8199 (tm-30) REVERT: H 93 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7917 (mt-10) REVERT: H 105 GLU cc_start: 0.8310 (tp30) cc_final: 0.7992 (tp30) REVERT: M 17 PRO cc_start: 0.8039 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: M 18 MET cc_start: 0.8731 (mmm) cc_final: 0.8427 (mmm) REVERT: M 28 TRP cc_start: 0.7930 (t60) cc_final: 0.7659 (t60) REVERT: M 51 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7662 (t-90) REVERT: M 74 MET cc_start: 0.8714 (tpp) cc_final: 0.8462 (tpp) REVERT: M 79 HIS cc_start: 0.8311 (p-80) cc_final: 0.7711 (m90) REVERT: M 88 MET cc_start: 0.6408 (ttm) cc_final: 0.5612 (tmm) REVERT: M 137 TRP cc_start: 0.8543 (m100) cc_final: 0.8205 (m100) REVERT: M 171 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7098 (t0) outliers start: 37 outliers final: 26 residues processed: 227 average time/residue: 0.2931 time to fit residues: 95.3159 Evaluate side-chains 220 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 47 SER 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 62 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 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 E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 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 G 84 GLN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.092824 restraints weight = 23622.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096322 restraints weight = 11553.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098612 restraints weight = 7701.517| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4586 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= 0.146 Angle : 0.587 9.453 21353 Z= 0.343 Chirality : 0.035 0.150 2418 Planarity : 0.004 0.044 1677 Dihedral : 29.738 142.162 4410 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.73 % Allowed : 20.24 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.26), residues: 979 helix: -1.07 (0.21), residues: 568 sheet: -0.01 (0.97), residues: 26 loop : -2.10 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 531 HIS 0.010 0.001 HIS D 82 PHE 0.012 0.001 PHE B 100 TYR 0.014 0.001 TYR D 40 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 451) hydrogen bonds : angle 3.20153 ( 1181) covalent geometry : bond 0.00313 (14874) covalent geometry : angle 0.58748 (21353) *********************** 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 237 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ILE cc_start: 0.8571 (mm) cc_final: 0.8151 (mm) REVERT: C 24 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8200 (mp10) REVERT: C 38 ASN cc_start: 0.7817 (m-40) cc_final: 0.7572 (p0) REVERT: C 39 TYR cc_start: 0.8807 (m-80) cc_final: 0.8573 (m-80) REVERT: C 41 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7491 (tt0) REVERT: D 62 MET cc_start: 0.9121 (tpp) cc_final: 0.8919 (tpp) REVERT: D 86 ARG cc_start: 0.6893 (mpt-90) cc_final: 0.6001 (mtp180) REVERT: E 80 ARG cc_start: 0.8521 (pmt170) cc_final: 0.7366 (mmt90) REVERT: F 44 LYS cc_start: 0.7665 (tttt) cc_final: 0.7232 (tptm) REVERT: F 74 GLU cc_start: 0.8363 (tt0) cc_final: 0.8117 (tp30) REVERT: F 92 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7468 (tmm-80) REVERT: G 20 ARG cc_start: 0.9231 (ttt180) cc_final: 0.8865 (tpt-90) REVERT: G 36 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7558 (tmtt) REVERT: G 38 ASN cc_start: 0.8845 (m-40) cc_final: 0.8574 (p0) REVERT: G 41 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7882 (tm-30) REVERT: G 51 LEU cc_start: 0.7915 (tp) cc_final: 0.7660 (tt) REVERT: G 56 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7612 (tm-30) REVERT: G 85 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8286 (tt) REVERT: H 71 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8240 (tm-30) REVERT: H 105 GLU cc_start: 0.8277 (tp30) cc_final: 0.8038 (tp30) REVERT: H 113 GLU cc_start: 0.7915 (tm-30) cc_final: 0.6972 (tm-30) REVERT: M 1 MET cc_start: 0.0643 (mpp) cc_final: -0.1127 (tpt) REVERT: M 3 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 17 PRO cc_start: 0.7785 (Cg_exo) cc_final: 0.7447 (Cg_endo) REVERT: M 18 MET cc_start: 0.8644 (mmm) cc_final: 0.8341 (mmm) REVERT: M 28 TRP cc_start: 0.7970 (t60) cc_final: 0.7643 (t60) REVERT: M 74 MET cc_start: 0.8715 (tpp) cc_final: 0.8513 (tpp) REVERT: M 79 HIS cc_start: 0.8238 (p-80) cc_final: 0.7712 (m90) REVERT: M 88 MET cc_start: 0.6334 (ttm) cc_final: 0.5519 (tmm) REVERT: M 131 VAL cc_start: 0.8047 (p) cc_final: 0.7823 (m) REVERT: M 137 TRP cc_start: 0.8541 (m100) cc_final: 0.8284 (m100) REVERT: M 171 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7128 (t0) outliers start: 31 outliers final: 22 residues processed: 223 average time/residue: 0.2701 time to fit residues: 86.5537 Evaluate side-chains 213 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL 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 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 80 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 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094126 restraints weight = 23709.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097652 restraints weight = 11759.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099971 restraints weight = 7868.494| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.143 Angle : 0.580 11.054 21353 Z= 0.336 Chirality : 0.035 0.146 2418 Planarity : 0.003 0.038 1677 Dihedral : 29.617 141.689 4410 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.73 % Allowed : 21.69 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.26), residues: 979 helix: -0.67 (0.22), residues: 565 sheet: 0.33 (1.04), residues: 26 loop : -2.00 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 531 HIS 0.006 0.001 HIS B 75 PHE 0.016 0.001 PHE B 100 TYR 0.024 0.002 TYR H 83 ARG 0.007 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 451) hydrogen bonds : angle 3.12930 ( 1181) covalent geometry : bond 0.00306 (14874) covalent geometry : angle 0.58038 (21353) *********************** 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 230 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7153 (mtm-85) REVERT: A 131 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7156 (ttt180) REVERT: B 29 ILE cc_start: 0.8535 (mm) cc_final: 0.8253 (mm) REVERT: C 24 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8259 (mp10) REVERT: C 38 ASN cc_start: 0.7929 (m-40) cc_final: 0.7618 (p0) REVERT: C 39 TYR cc_start: 0.8781 (m-80) cc_final: 0.8550 (m-80) REVERT: C 41 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7543 (tt0) REVERT: D 42 TYR cc_start: 0.7091 (t80) cc_final: 0.6887 (t80) REVERT: D 86 ARG cc_start: 0.6806 (mpt-90) cc_final: 0.5883 (mtp180) REVERT: E 80 ARG cc_start: 0.8592 (pmt170) cc_final: 0.7495 (mmt90) REVERT: E 95 GLN cc_start: 0.8106 (tt0) cc_final: 0.7648 (tp40) REVERT: E 96 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8389 (mm-30) REVERT: F 92 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.7473 (tmm-80) REVERT: G 20 ARG cc_start: 0.9221 (ttt180) cc_final: 0.8860 (tpt-90) REVERT: G 36 LYS cc_start: 0.7989 (mmpt) cc_final: 0.7612 (tmtt) REVERT: G 38 ASN cc_start: 0.8789 (m-40) cc_final: 0.8519 (p0) REVERT: G 41 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7929 (tm-30) REVERT: G 51 LEU cc_start: 0.7879 (tp) cc_final: 0.7648 (tt) REVERT: G 56 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7575 (tm-30) REVERT: G 85 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8186 (tt) REVERT: H 71 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8166 (tm-30) REVERT: H 82 HIS cc_start: 0.8288 (t-90) cc_final: 0.7965 (t-90) REVERT: H 105 GLU cc_start: 0.8253 (tp30) cc_final: 0.8028 (tp30) REVERT: M 17 PRO cc_start: 0.7655 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: M 18 MET cc_start: 0.8435 (mmm) cc_final: 0.8096 (mmm) REVERT: M 28 TRP cc_start: 0.7987 (t60) cc_final: 0.7728 (t60) REVERT: M 33 GLU cc_start: 0.7707 (pm20) cc_final: 0.7399 (pm20) REVERT: M 74 MET cc_start: 0.8702 (tpp) cc_final: 0.8473 (tpp) REVERT: M 79 HIS cc_start: 0.8227 (p-80) cc_final: 0.7711 (m90) REVERT: M 88 MET cc_start: 0.6342 (ttm) cc_final: 0.5678 (tmm) REVERT: M 101 MET cc_start: 0.5926 (pmm) cc_final: 0.5632 (pmm) REVERT: M 131 VAL cc_start: 0.8027 (p) cc_final: 0.7787 (m) REVERT: M 137 TRP cc_start: 0.8591 (m100) cc_final: 0.8304 (m100) REVERT: M 171 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7137 (t0) outliers start: 31 outliers final: 21 residues processed: 219 average time/residue: 0.2550 time to fit residues: 81.0486 Evaluate side-chains 213 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG 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 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 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 171 ASN 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 56 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.183390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111516 restraints weight = 22389.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.114905 restraints weight = 11112.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117097 restraints weight = 7528.272| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14874 Z= 0.245 Angle : 0.682 10.890 21353 Z= 0.383 Chirality : 0.040 0.158 2418 Planarity : 0.004 0.047 1677 Dihedral : 29.673 134.989 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.42 % Allowed : 20.72 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 979 helix: -0.88 (0.21), residues: 578 sheet: 0.54 (1.02), residues: 26 loop : -2.12 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 531 HIS 0.010 0.001 HIS D 82 PHE 0.013 0.001 PHE B 100 TYR 0.024 0.002 TYR H 83 ARG 0.006 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 451) hydrogen bonds : angle 3.69302 ( 1181) covalent geometry : bond 0.00549 (14874) covalent geometry : angle 0.68215 (21353) *********************** 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 236 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8584 (mm-30) REVERT: A 125 ASP cc_start: 0.8177 (m-30) cc_final: 0.7941 (m-30) REVERT: B 29 ILE cc_start: 0.8678 (mm) cc_final: 0.8229 (mm) REVERT: C 24 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8354 (mm110) REVERT: C 38 ASN cc_start: 0.7786 (m-40) cc_final: 0.7387 (p0) REVERT: C 39 TYR cc_start: 0.8846 (m-80) cc_final: 0.8606 (m-80) REVERT: C 41 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7651 (tt0) REVERT: C 56 GLU cc_start: 0.8279 (tt0) cc_final: 0.7309 (tt0) REVERT: D 52 THR cc_start: 0.9240 (m) cc_final: 0.8722 (p) REVERT: D 82 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7665 (t70) REVERT: D 86 ARG cc_start: 0.7402 (mpt-90) cc_final: 0.6572 (mtp180) REVERT: E 65 LEU cc_start: 0.8487 (tp) cc_final: 0.8205 (tt) REVERT: E 80 ARG cc_start: 0.8588 (pmt170) cc_final: 0.7589 (mmt90) REVERT: E 95 GLN cc_start: 0.8343 (tt0) cc_final: 0.8010 (tp40) REVERT: E 99 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7837 (tm-30) REVERT: E 124 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7396 (ttpt) REVERT: F 92 ARG cc_start: 0.8508 (tmm-80) cc_final: 0.7749 (tmm-80) REVERT: G 20 ARG cc_start: 0.9316 (ttt180) cc_final: 0.8984 (tpt-90) REVERT: G 36 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7630 (tmtt) REVERT: G 38 ASN cc_start: 0.8907 (m-40) cc_final: 0.8499 (p0) REVERT: G 41 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8066 (tm-30) REVERT: G 56 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7686 (tm-30) REVERT: G 85 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8379 (tt) REVERT: H 71 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8227 (tm-30) REVERT: L 521 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7427 (tpp80) REVERT: M 1 MET cc_start: 0.1413 (mpp) cc_final: 0.1046 (mmt) REVERT: M 17 PRO cc_start: 0.7909 (Cg_exo) cc_final: 0.7637 (Cg_endo) REVERT: M 18 MET cc_start: 0.8302 (mmm) cc_final: 0.8056 (mmm) REVERT: M 28 TRP cc_start: 0.8033 (t60) cc_final: 0.7777 (t60) REVERT: M 33 GLU cc_start: 0.7787 (pm20) cc_final: 0.7508 (pm20) REVERT: M 74 MET cc_start: 0.8792 (tpp) cc_final: 0.8534 (tpp) REVERT: M 79 HIS cc_start: 0.8354 (p-80) cc_final: 0.7996 (m90) REVERT: M 101 MET cc_start: 0.6548 (pmm) cc_final: 0.6266 (pmm) REVERT: M 131 VAL cc_start: 0.7879 (p) cc_final: 0.7608 (m) REVERT: M 171 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7083 (t0) outliers start: 45 outliers final: 33 residues processed: 217 average time/residue: 0.2812 time to fit residues: 86.0153 Evaluate side-chains 222 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 54 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 82 HIS 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 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU 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 56 CYS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 171 ASN 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 43 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.156577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.093278 restraints weight = 23980.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096728 restraints weight = 12148.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099037 restraints weight = 8234.829| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14874 Z= 0.147 Angle : 0.600 11.129 21353 Z= 0.344 Chirality : 0.035 0.156 2418 Planarity : 0.004 0.052 1677 Dihedral : 29.628 140.194 4410 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.25 % Allowed : 23.25 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 979 helix: -0.62 (0.21), residues: 582 sheet: 1.01 (1.03), residues: 26 loop : -2.12 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 531 HIS 0.015 0.001 HIS D 82 PHE 0.018 0.001 PHE B 100 TYR 0.024 0.002 TYR H 83 ARG 0.009 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 451) hydrogen bonds : angle 3.16763 ( 1181) covalent geometry : bond 0.00317 (14874) covalent geometry : angle 0.60011 (21353) *********************** 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 219 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6556 (mtm180) REVERT: A 131 ARG cc_start: 0.7657 (ttt90) cc_final: 0.7450 (ttt90) REVERT: B 29 ILE cc_start: 0.8512 (mm) cc_final: 0.8297 (mm) REVERT: C 24 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8136 (mp10) REVERT: C 38 ASN cc_start: 0.7731 (m-40) cc_final: 0.7507 (p0) REVERT: C 39 TYR cc_start: 0.8793 (m-80) cc_final: 0.8581 (m-80) REVERT: C 41 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7566 (tt0) REVERT: C 56 GLU cc_start: 0.8074 (tt0) cc_final: 0.7076 (tt0) REVERT: C 71 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8064 (ttm-80) REVERT: D 37 TYR cc_start: 0.8695 (m-80) cc_final: 0.8333 (m-80) REVERT: D 42 TYR cc_start: 0.7124 (t80) cc_final: 0.6898 (t80) REVERT: D 86 ARG cc_start: 0.6967 (mpt-90) cc_final: 0.6084 (mtp180) REVERT: E 80 ARG cc_start: 0.8573 (pmt170) cc_final: 0.7476 (mmt90) REVERT: E 99 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7751 (tm-30) REVERT: F 47 SER cc_start: 0.8975 (t) cc_final: 0.8342 (m) REVERT: G 20 ARG cc_start: 0.9214 (ttt180) cc_final: 0.8848 (tpt-90) REVERT: G 36 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7640 (tmtt) REVERT: G 38 ASN cc_start: 0.8861 (m-40) cc_final: 0.8627 (p0) REVERT: G 41 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7990 (tm-30) REVERT: G 56 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7554 (tm-30) REVERT: G 85 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (tt) REVERT: H 35 GLU cc_start: 0.7296 (mp0) cc_final: 0.7057 (mp0) REVERT: H 71 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8237 (tm-30) REVERT: H 82 HIS cc_start: 0.8332 (t-90) cc_final: 0.7943 (t-90) REVERT: M 1 MET cc_start: 0.1090 (mpp) cc_final: 0.0780 (mmt) REVERT: M 3 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7517 (tm-30) REVERT: M 17 PRO cc_start: 0.7600 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: M 18 MET cc_start: 0.8224 (mmm) cc_final: 0.7881 (mmm) REVERT: M 28 TRP cc_start: 0.7948 (t60) cc_final: 0.7738 (t60) REVERT: M 33 GLU cc_start: 0.7737 (pm20) cc_final: 0.7478 (pm20) REVERT: M 74 MET cc_start: 0.8775 (tpp) cc_final: 0.8543 (tpp) REVERT: M 79 HIS cc_start: 0.8270 (p-80) cc_final: 0.7897 (m90) REVERT: M 101 MET cc_start: 0.6682 (pmm) cc_final: 0.6426 (pmm) REVERT: M 131 VAL cc_start: 0.7971 (p) cc_final: 0.7726 (m) REVERT: M 137 TRP cc_start: 0.8549 (m100) cc_final: 0.8193 (m100) REVERT: M 171 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7108 (t0) REVERT: M 180 THR cc_start: 0.7651 (m) cc_final: 0.7015 (m) outliers start: 27 outliers final: 21 residues processed: 207 average time/residue: 0.2735 time to fit residues: 80.9685 Evaluate side-chains 207 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 73 THR 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR 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 171 ASN Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 197 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 118 optimal weight: 40.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN D 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116052 restraints weight = 22572.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.119715 restraints weight = 10981.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.122101 restraints weight = 7342.094| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14874 Z= 0.145 Angle : 0.600 11.457 21353 Z= 0.339 Chirality : 0.035 0.154 2418 Planarity : 0.004 0.044 1677 Dihedral : 29.544 139.143 4410 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.01 % Allowed : 24.10 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 979 helix: -0.31 (0.22), residues: 585 sheet: 0.98 (1.03), residues: 26 loop : -2.03 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 531 HIS 0.011 0.001 HIS D 82 PHE 0.013 0.001 PHE B 100 TYR 0.023 0.002 TYR H 83 ARG 0.010 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 451) hydrogen bonds : angle 3.15141 ( 1181) covalent geometry : bond 0.00312 (14874) covalent geometry : angle 0.59970 (21353) *********************** 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 216 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6572 (mtm180) REVERT: A 99 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: B 29 ILE cc_start: 0.8575 (mm) cc_final: 0.8034 (mm) REVERT: B 47 SER cc_start: 0.9280 (t) cc_final: 0.8978 (m) REVERT: B 84 MET cc_start: 0.7627 (tpp) cc_final: 0.7372 (tpt) REVERT: C 24 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8122 (mp10) REVERT: C 38 ASN cc_start: 0.7809 (m-40) cc_final: 0.7567 (p0) REVERT: C 41 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7556 (tt0) REVERT: C 56 GLU cc_start: 0.8053 (tt0) cc_final: 0.7093 (tt0) REVERT: C 71 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8035 (ttm-80) REVERT: D 37 TYR cc_start: 0.8774 (m-80) cc_final: 0.8440 (m-80) REVERT: D 42 TYR cc_start: 0.7222 (t80) cc_final: 0.6986 (t80) REVERT: D 52 THR cc_start: 0.9127 (m) cc_final: 0.8388 (p) REVERT: D 86 ARG cc_start: 0.6987 (mpt-90) cc_final: 0.6132 (mtp180) REVERT: F 92 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.8128 (tmm-80) REVERT: G 36 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7561 (tmtt) REVERT: G 38 ASN cc_start: 0.8823 (m-40) cc_final: 0.8552 (p0) REVERT: G 41 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7997 (tm-30) REVERT: G 56 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7671 (tm-30) REVERT: G 85 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8281 (tt) REVERT: H 35 GLU cc_start: 0.7319 (mp0) cc_final: 0.7029 (mp0) REVERT: H 71 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8225 (tm-30) REVERT: H 82 HIS cc_start: 0.8268 (t-90) cc_final: 0.7867 (t-90) REVERT: M 3 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7605 (tm-30) REVERT: M 18 MET cc_start: 0.8128 (mmm) cc_final: 0.7876 (mmm) REVERT: M 28 TRP cc_start: 0.8080 (t60) cc_final: 0.7838 (t60) REVERT: M 74 MET cc_start: 0.8752 (tpp) cc_final: 0.8537 (tpp) REVERT: M 79 HIS cc_start: 0.8325 (p-80) cc_final: 0.7931 (m90) REVERT: M 101 MET cc_start: 0.6755 (pmm) cc_final: 0.6486 (pmm) REVERT: M 131 VAL cc_start: 0.8065 (p) cc_final: 0.7834 (m) REVERT: M 171 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.6959 (t0) outliers start: 25 outliers final: 19 residues processed: 202 average time/residue: 0.2930 time to fit residues: 85.2185 Evaluate side-chains 200 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 73 THR 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain 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 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 87 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** 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 = 0.4470 r_free = 0.4470 target = 0.186343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113831 restraints weight = 22644.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117503 restraints weight = 10952.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119897 restraints weight = 7298.460| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5676 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= 0.161 Angle : 0.611 11.713 21353 Z= 0.345 Chirality : 0.036 0.150 2418 Planarity : 0.004 0.047 1677 Dihedral : 29.554 138.679 4410 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.25 % Allowed : 23.61 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 979 helix: -0.12 (0.22), residues: 579 sheet: 1.25 (1.07), residues: 26 loop : -1.95 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 531 HIS 0.010 0.001 HIS M 185 PHE 0.019 0.001 PHE M 8 TYR 0.026 0.002 TYR H 83 ARG 0.009 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 451) hydrogen bonds : angle 3.24061 ( 1181) covalent geometry : bond 0.00354 (14874) covalent geometry : angle 0.61104 (21353) ********************** 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 209 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6592 (mtm180) REVERT: B 29 ILE cc_start: 0.8387 (mm) cc_final: 0.8026 (mm) REVERT: B 47 SER cc_start: 0.9267 (t) cc_final: 0.8981 (m) REVERT: C 24 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8080 (mp10) REVERT: C 38 ASN cc_start: 0.7730 (m-40) cc_final: 0.7465 (p0) REVERT: C 39 TYR cc_start: 0.8393 (m-80) cc_final: 0.8116 (m-80) REVERT: C 41 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7561 (tt0) REVERT: C 56 GLU cc_start: 0.8073 (tt0) cc_final: 0.7076 (tt0) REVERT: C 71 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8041 (ttm-80) REVERT: D 37 TYR cc_start: 0.8762 (m-80) cc_final: 0.8397 (m-80) REVERT: D 52 THR cc_start: 0.9125 (m) cc_final: 0.8381 (p) REVERT: D 82 HIS cc_start: 0.7958 (t70) cc_final: 0.7731 (t-170) REVERT: D 86 ARG cc_start: 0.7066 (mpt-90) cc_final: 0.6187 (mtp180) REVERT: F 92 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8115 (tmm-80) REVERT: G 36 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7615 (tmtt) REVERT: G 38 ASN cc_start: 0.8841 (m-40) cc_final: 0.8556 (p0) REVERT: G 41 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8005 (tm-30) REVERT: G 56 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7671 (tm-30) REVERT: G 85 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (tt) REVERT: H 35 GLU cc_start: 0.7306 (mp0) cc_final: 0.7007 (mp0) REVERT: H 71 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8190 (tm-30) REVERT: H 82 HIS cc_start: 0.8293 (t-90) cc_final: 0.7887 (t-90) REVERT: M 3 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7616 (tm-30) REVERT: M 18 MET cc_start: 0.8143 (mmm) cc_final: 0.7865 (mmm) REVERT: M 74 MET cc_start: 0.8762 (tpp) cc_final: 0.8539 (tpp) REVERT: M 79 HIS cc_start: 0.8296 (p-80) cc_final: 0.7893 (m90) REVERT: M 101 MET cc_start: 0.6830 (pmm) cc_final: 0.6575 (pmm) REVERT: M 131 VAL cc_start: 0.8013 (p) cc_final: 0.7771 (m) REVERT: M 171 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.6950 (t0) outliers start: 27 outliers final: 21 residues processed: 196 average time/residue: 0.2557 time to fit residues: 72.8989 Evaluate side-chains 204 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 73 THR 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain 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 171 ASN Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.185707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.112153 restraints weight = 22980.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115809 restraints weight = 11236.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118199 restraints weight = 7547.696| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5732 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= 0.162 Angle : 0.617 11.822 21353 Z= 0.347 Chirality : 0.036 0.159 2418 Planarity : 0.004 0.044 1677 Dihedral : 29.558 138.337 4410 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.25 % Allowed : 24.22 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 979 helix: -0.02 (0.22), residues: 580 sheet: 1.28 (1.08), residues: 26 loop : -1.99 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP M 28 HIS 0.008 0.001 HIS M 185 PHE 0.021 0.001 PHE M 8 TYR 0.026 0.002 TYR H 83 ARG 0.018 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 451) hydrogen bonds : angle 3.25680 ( 1181) covalent geometry : bond 0.00356 (14874) covalent geometry : angle 0.61655 (21353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.90 seconds wall clock time: 83 minutes 27.49 seconds (5007.49 seconds total)