Starting phenix.real_space_refine on Thu Nov 16 02:49:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_9250_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_9250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_9250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_9250_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/11_2023/6muo_9250_neut.pdb" } 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 Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 526": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 169": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.88, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 7.64 Conformation dependent library (CDL) restraints added in 3.5 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: 5.87 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: 4.76 Time building geometry restraints manager: 7.26 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: 91.77 - 102.99: 406 102.99 - 114.20: 10131 114.20 - 125.41: 9731 125.41 - 136.62: 1084 136.62 - 147.84: 1 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: 6579 35.98 - 71.96: 1267 71.96 - 107.93: 33 107.93 - 143.91: 0 143.91 - 179.89: 1 Dihedral angle restraints: 7880 sinusoidal: 4963 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 7877 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 2.520 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.116 2.520 nonbonded pdb=" OD2 ASP M 70 " pdb=" OH TYR M 151 " model vdw 2.129 2.440 nonbonded pdb=" NH1 ARG A 130 " pdb=" O TRP L 531 " model vdw 2.151 2.520 nonbonded pdb=" NH1 ARG B 23 " pdb=" OP1 DT J 16 " model vdw 2.157 2.520 ... (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 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: 0.370 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: 0.020 Extract box with map and model: 2.550 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.870 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- 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= 0.480 Angle : 0.953 26.818 21353 Z= 0.582 Chirality : 0.047 0.298 2418 Planarity : 0.006 0.062 1677 Dihedral : 26.185 179.887 5990 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 343 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 346 average time/residue: 0.3234 time to fit residues: 148.3260 Evaluate side-chains 206 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1201 time to fit residues: 1.5730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 E 59 HIS G 31 HIS G 73 ASN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14874 Z= 0.300 Angle : 0.732 7.889 21353 Z= 0.421 Chirality : 0.042 0.249 2418 Planarity : 0.005 0.038 1677 Dihedral : 30.755 161.096 4054 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.22 % Allowed : 14.22 % Favored : 81.57 % 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: -4.50 (0.21), residues: 979 helix: -3.06 (0.16), residues: 569 sheet: -1.31 (0.90), residues: 26 loop : -2.75 (0.28), residues: 384 *********************** 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 258 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 242 average time/residue: 0.2874 time to fit residues: 97.0171 Evaluate side-chains 211 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1210 time to fit residues: 6.6305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 82 HIS D 47 GLN D 82 HIS E 59 HIS E 95 GLN H 47 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14874 Z= 0.298 Angle : 0.694 7.795 21353 Z= 0.400 Chirality : 0.040 0.184 2418 Planarity : 0.005 0.063 1677 Dihedral : 30.653 146.733 4054 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.10 % Allowed : 18.43 % Favored : 77.47 % 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: -3.58 (0.24), residues: 979 helix: -2.18 (0.19), residues: 565 sheet: -0.74 (0.96), residues: 26 loop : -2.63 (0.29), residues: 388 *********************** 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 245 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 225 average time/residue: 0.2804 time to fit residues: 88.3736 Evaluate side-chains 204 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1174 time to fit residues: 5.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 0.0040 chunk 118 optimal weight: 40.0000 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 G 84 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14874 Z= 0.173 Angle : 0.608 8.546 21353 Z= 0.353 Chirality : 0.036 0.182 2418 Planarity : 0.004 0.052 1677 Dihedral : 30.475 143.693 4054 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.65 % Allowed : 20.72 % Favored : 76.63 % 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: -2.76 (0.25), residues: 979 helix: -1.46 (0.20), residues: 562 sheet: -0.27 (1.03), residues: 26 loop : -2.38 (0.29), residues: 391 *********************** 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 240 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 218 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 226 average time/residue: 0.2740 time to fit residues: 88.2288 Evaluate side-chains 204 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1187 time to fit residues: 4.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN D 47 GLN D 82 HIS E 59 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14874 Z= 0.245 Angle : 0.640 9.931 21353 Z= 0.366 Chirality : 0.037 0.160 2418 Planarity : 0.004 0.049 1677 Dihedral : 30.390 139.078 4054 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.98 % Allowed : 21.81 % Favored : 74.22 % 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: -2.52 (0.25), residues: 979 helix: -1.20 (0.21), residues: 567 sheet: 0.09 (1.07), residues: 26 loop : -2.42 (0.29), residues: 386 *********************** 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 227 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 209 average time/residue: 0.2709 time to fit residues: 81.9437 Evaluate side-chains 207 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1228 time to fit residues: 6.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 104 HIS D 47 GLN E 59 HIS E 95 GLN E 104 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN M 50 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14874 Z= 0.304 Angle : 0.676 10.512 21353 Z= 0.384 Chirality : 0.039 0.163 2418 Planarity : 0.004 0.058 1677 Dihedral : 30.370 136.411 4054 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.01 % Allowed : 22.77 % Favored : 74.22 % 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: -2.42 (0.25), residues: 979 helix: -1.08 (0.21), residues: 553 sheet: -1.10 (0.99), residues: 33 loop : -2.33 (0.29), residues: 393 *********************** 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 222 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 206 average time/residue: 0.2685 time to fit residues: 79.6871 Evaluate side-chains 203 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1283 time to fit residues: 5.8706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 38 ASN D 82 HIS E 59 HIS E 95 GLN E 104 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14874 Z= 0.253 Angle : 0.650 11.014 21353 Z= 0.370 Chirality : 0.038 0.157 2418 Planarity : 0.004 0.059 1677 Dihedral : 30.345 136.236 4054 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.93 % Allowed : 25.42 % Favored : 72.65 % 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: -2.30 (0.26), residues: 979 helix: -1.01 (0.21), residues: 566 sheet: -0.83 (1.01), residues: 33 loop : -2.27 (0.31), residues: 380 *********************** 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 210 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 199 average time/residue: 0.3050 time to fit residues: 85.3147 Evaluate side-chains 199 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1300 time to fit residues: 4.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 HIS E 95 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.004 0.043 14874 Z= 0.217 Angle : 0.631 11.175 21353 Z= 0.360 Chirality : 0.037 0.156 2418 Planarity : 0.004 0.057 1677 Dihedral : 30.314 136.142 4054 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.69 % Allowed : 26.14 % Favored : 72.17 % 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: -1.97 (0.26), residues: 979 helix: -0.70 (0.22), residues: 554 sheet: -1.02 (0.97), residues: 35 loop : -2.16 (0.30), residues: 390 *********************** 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 209 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 201 average time/residue: 0.2693 time to fit residues: 77.7236 Evaluate side-chains 191 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1214 time to fit residues: 3.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 113 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 95 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5631 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= 0.175 Angle : 0.608 11.741 21353 Z= 0.346 Chirality : 0.035 0.178 2418 Planarity : 0.004 0.051 1677 Dihedral : 30.238 137.596 4054 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.45 % Allowed : 25.90 % Favored : 72.65 % 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: -1.61 (0.27), residues: 979 helix: -0.36 (0.22), residues: 562 sheet: -1.06 (0.94), residues: 35 loop : -2.07 (0.31), residues: 382 *********************** 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 209 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 200 average time/residue: 0.2665 time to fit residues: 76.7599 Evaluate side-chains 193 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1282 time to fit residues: 3.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN D 47 GLN D 82 HIS E 59 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.5615 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= 0.288 Angle : 0.681 11.967 21353 Z= 0.381 Chirality : 0.039 0.175 2418 Planarity : 0.004 0.057 1677 Dihedral : 30.277 133.420 4054 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.48 % Allowed : 27.23 % Favored : 72.29 % 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: -1.89 (0.27), residues: 979 helix: -0.59 (0.22), residues: 572 sheet: -1.00 (0.93), residues: 35 loop : -2.24 (0.31), residues: 372 ********************** 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 190 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 187 average time/residue: 0.2876 time to fit residues: 76.3158 Evaluate side-chains 182 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1288 time to fit residues: 1.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0980 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093952 restraints weight = 23832.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097428 restraints weight = 11914.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099713 restraints weight = 8008.861| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5955 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= 0.174 Angle : 0.626 12.609 21353 Z= 0.352 Chirality : 0.035 0.169 2418 Planarity : 0.004 0.051 1677 Dihedral : 30.253 137.766 4054 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.48 % Allowed : 28.31 % Favored : 71.20 % 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: -1.37 (0.27), residues: 979 helix: -0.18 (0.22), residues: 571 sheet: -0.85 (0.94), residues: 35 loop : -2.01 (0.32), residues: 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.57 seconds wall clock time: 48 minutes 23.47 seconds (2903.47 seconds total)