Starting phenix.real_space_refine on Sat Mar 16 07:05:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/03_2024/6muo_9250_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/03_2024/6muo_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_9250/03_2024/6muo_9250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/03_2024/6muo_9250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/03_2024/6muo_9250_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muo_9250/03_2024/6muo_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-dev-5265/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: 7.28, per 1000 atoms: 0.52 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: 6.81 Conformation dependent library (CDL) restraints added in 1.5 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: 5.74 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: 4.63 Time building geometry restraints manager: 7.22 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: 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 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: 0.490 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: 2.450 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.680 Find NCS groups from input model: 0.540 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- 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 : 26.213 179.887 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 *********************** 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 : 1.019 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: 0.3324 time to fit residues: 152.6510 Evaluate side-chains 218 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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: 9.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 E 104 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14874 Z= 0.299 Angle : 0.728 7.352 21353 Z= 0.421 Chirality : 0.042 0.274 2418 Planarity : 0.005 0.037 1677 Dihedral : 30.257 157.182 4415 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.22 % Allowed : 13.98 % Favored : 81.81 % 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: -4.44 (0.21), residues: 979 helix: -2.94 (0.16), residues: 569 sheet: -1.35 (0.86), residues: 28 loop : -2.84 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 531 HIS 0.013 0.002 HIS D 82 PHE 0.017 0.002 PHE F 100 TYR 0.035 0.002 TYR D 40 ARG 0.005 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6522 (mmt-90) cc_final: 0.5847 (mmm-85) REVERT: A 92 LEU cc_start: 0.7861 (mt) cc_final: 0.7073 (tt) REVERT: A 137 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6592 (mt-10) REVERT: B 27 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7507 (mm-40) REVERT: B 29 ILE cc_start: 0.8048 (mm) cc_final: 0.7631 (mm) REVERT: B 40 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7862 (mmm-85) REVERT: C 24 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7872 (mp10) REVERT: C 38 ASN cc_start: 0.7523 (m-40) cc_final: 0.7309 (p0) REVERT: C 39 TYR cc_start: 0.8489 (m-80) cc_final: 0.8239 (m-80) REVERT: C 41 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7847 (tt0) REVERT: C 56 GLU cc_start: 0.7099 (tt0) cc_final: 0.6379 (tt0) REVERT: C 72 ASP cc_start: 0.8944 (t70) cc_final: 0.8730 (m-30) REVERT: C 107 VAL cc_start: 0.8056 (m) cc_final: 0.7845 (p) REVERT: D 52 THR cc_start: 0.9003 (m) cc_final: 0.8431 (p) REVERT: D 82 HIS cc_start: 0.8052 (t-90) cc_final: 0.7793 (t-170) REVERT: D 86 ARG cc_start: 0.7130 (mpt-90) cc_final: 0.6265 (mtp180) REVERT: E 65 LEU cc_start: 0.8039 (tp) cc_final: 0.7836 (tt) REVERT: E 80 ARG cc_start: 0.8731 (pmt170) cc_final: 0.7656 (mmt90) REVERT: E 104 HIS cc_start: 0.7996 (t-90) cc_final: 0.7616 (t70) REVERT: E 136 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 84 MET cc_start: 0.7119 (tpt) cc_final: 0.6702 (mmt) REVERT: G 20 ARG cc_start: 0.9220 (ttt180) cc_final: 0.8899 (tpt-90) REVERT: G 36 LYS cc_start: 0.7788 (mmpt) cc_final: 0.7342 (tmtt) REVERT: G 41 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 99 ARG cc_start: 0.7991 (mmt180) cc_final: 0.6905 (mtm180) REVERT: H 62 MET cc_start: 0.8275 (mmm) cc_final: 0.7820 (mmp) REVERT: H 93 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7829 (mt-10) REVERT: M 50 GLN cc_start: 0.7971 (mt0) cc_final: 0.7708 (tt0) REVERT: M 51 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8056 (t-90) REVERT: M 74 MET cc_start: 0.8840 (tpp) cc_final: 0.8498 (tpt) REVERT: M 79 HIS cc_start: 0.8543 (p-80) cc_final: 0.7939 (m90) REVERT: M 133 ILE cc_start: 0.6244 (mt) cc_final: 0.5980 (tp) REVERT: M 162 PHE cc_start: 0.8907 (m-10) cc_final: 0.8671 (m-80) REVERT: M 171 ASN cc_start: 0.7880 (t160) cc_final: 0.7103 (t0) outliers start: 35 outliers final: 25 residues processed: 258 average time/residue: 0.2817 time to fit residues: 100.9025 Evaluate side-chains 227 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 41 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 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 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 E 59 HIS G 84 GLN H 47 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3670 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= 0.274 Angle : 0.675 7.592 21353 Z= 0.389 Chirality : 0.039 0.181 2418 Planarity : 0.005 0.065 1677 Dihedral : 30.045 147.810 4412 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 6.27 % Allowed : 17.23 % Favored : 76.51 % 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: -3.49 (0.24), residues: 979 helix: -2.10 (0.19), residues: 567 sheet: -0.77 (0.89), residues: 28 loop : -2.61 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 28 HIS 0.011 0.001 HIS B 75 PHE 0.013 0.002 PHE B 100 TYR 0.022 0.002 TYR E 110 ARG 0.006 0.001 ARG G 81 *********************** 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 270 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7821 (mt) cc_final: 0.7095 (tt) REVERT: A 137 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6600 (mt-10) REVERT: B 29 ILE cc_start: 0.8125 (mm) cc_final: 0.7899 (mm) REVERT: B 40 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7958 (mmm-85) REVERT: C 24 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7932 (mp10) REVERT: C 38 ASN cc_start: 0.7438 (m-40) cc_final: 0.7130 (p0) REVERT: C 39 TYR cc_start: 0.8447 (m-80) cc_final: 0.8177 (m-80) REVERT: C 41 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7505 (tt0) REVERT: C 56 GLU cc_start: 0.7174 (tt0) cc_final: 0.6480 (tt0) REVERT: C 64 GLU cc_start: 0.7830 (tt0) cc_final: 0.7573 (tt0) REVERT: C 74 LYS cc_start: 0.8577 (mptt) cc_final: 0.8369 (mmtp) REVERT: D 52 THR cc_start: 0.8997 (m) cc_final: 0.8414 (p) REVERT: D 86 ARG cc_start: 0.7291 (mpt-90) cc_final: 0.6471 (mtp180) REVERT: E 65 LEU cc_start: 0.7996 (tp) cc_final: 0.7795 (tt) REVERT: E 80 ARG cc_start: 0.8677 (pmt170) cc_final: 0.7536 (mmt90) REVERT: E 104 HIS cc_start: 0.7894 (t-90) cc_final: 0.7465 (t70) REVERT: E 122 PHE cc_start: 0.7361 (m-80) cc_final: 0.7140 (m-80) REVERT: E 136 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7962 (mm-30) REVERT: F 29 ILE cc_start: 0.8283 (mm) cc_final: 0.8022 (mm) REVERT: F 98 TYR cc_start: 0.7891 (m-10) cc_final: 0.7675 (m-80) REVERT: G 20 ARG cc_start: 0.9208 (ttt180) cc_final: 0.8941 (tpt-90) REVERT: G 36 LYS cc_start: 0.7779 (mmpt) cc_final: 0.7357 (tmtt) REVERT: G 38 ASN cc_start: 0.9077 (m-40) cc_final: 0.8463 (p0) REVERT: G 41 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7927 (tm-30) REVERT: G 99 ARG cc_start: 0.8090 (mmt180) cc_final: 0.6967 (mtm180) REVERT: H 48 VAL cc_start: 0.8834 (t) cc_final: 0.8633 (p) REVERT: H 93 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7648 (mt-10) REVERT: L 521 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7597 (tpp-160) REVERT: M 3 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8014 (tm-30) REVERT: M 19 ASN cc_start: 0.9416 (t0) cc_final: 0.9190 (t0) REVERT: M 51 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8082 (t-90) REVERT: M 74 MET cc_start: 0.8788 (tpp) cc_final: 0.8587 (tpt) REVERT: M 79 HIS cc_start: 0.8482 (p-80) cc_final: 0.7973 (m90) REVERT: M 101 MET cc_start: 0.5583 (mtp) cc_final: 0.5154 (mpp) REVERT: M 150 THR cc_start: 0.8515 (m) cc_final: 0.8311 (p) REVERT: M 151 TYR cc_start: 0.8273 (m-10) cc_final: 0.8059 (m-10) REVERT: M 171 ASN cc_start: 0.7810 (t160) cc_final: 0.7265 (t0) outliers start: 52 outliers final: 39 residues processed: 242 average time/residue: 0.2740 time to fit residues: 93.9081 Evaluate side-chains 238 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 47 SER 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 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 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 F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 90 THR 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 68 LEU Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 106 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 82 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4245 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= 0.169 Angle : 0.591 9.020 21353 Z= 0.346 Chirality : 0.035 0.162 2418 Planarity : 0.004 0.054 1677 Dihedral : 29.860 145.257 4412 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 22.05 % Favored : 75.18 % 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: -2.73 (0.25), residues: 979 helix: -1.43 (0.21), residues: 569 sheet: 0.03 (0.95), residues: 26 loop : -2.41 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 137 HIS 0.010 0.001 HIS D 82 PHE 0.016 0.001 PHE F 100 TYR 0.022 0.001 TYR E 110 ARG 0.009 0.001 ARG C 71 *********************** 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 241 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.5955 (mmt-90) cc_final: 0.5571 (mmm-85) REVERT: B 29 ILE cc_start: 0.7945 (mm) cc_final: 0.7464 (mm) REVERT: C 38 ASN cc_start: 0.7510 (m-40) cc_final: 0.7258 (p0) REVERT: C 39 TYR cc_start: 0.8386 (m-80) cc_final: 0.8157 (m-80) REVERT: C 41 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7510 (tt0) REVERT: C 56 GLU cc_start: 0.7047 (tt0) cc_final: 0.6821 (tt0) REVERT: C 64 GLU cc_start: 0.7829 (tt0) cc_final: 0.7598 (tt0) REVERT: D 86 ARG cc_start: 0.6933 (mpt-90) cc_final: 0.6053 (mtp180) REVERT: E 80 ARG cc_start: 0.8551 (pmt170) cc_final: 0.7344 (mmt90) REVERT: E 96 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8289 (mm-30) REVERT: E 104 HIS cc_start: 0.7624 (t-90) cc_final: 0.7213 (t70) REVERT: E 122 PHE cc_start: 0.7213 (m-80) cc_final: 0.6923 (m-10) REVERT: E 135 LEU cc_start: 0.7352 (tt) cc_final: 0.6955 (tt) REVERT: F 29 ILE cc_start: 0.8219 (mm) cc_final: 0.7892 (mm) REVERT: F 84 MET cc_start: 0.7085 (tpt) cc_final: 0.6417 (mmt) REVERT: F 92 ARG cc_start: 0.7574 (tmm-80) cc_final: 0.7240 (tmm-80) REVERT: F 97 LEU cc_start: 0.7989 (tp) cc_final: 0.7775 (tp) REVERT: F 98 TYR cc_start: 0.7843 (m-10) cc_final: 0.7501 (m-80) REVERT: G 36 LYS cc_start: 0.7627 (mmpt) cc_final: 0.7238 (tmtt) REVERT: G 38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8546 (p0) REVERT: G 41 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7861 (tm-30) REVERT: G 51 LEU cc_start: 0.7569 (tp) cc_final: 0.7295 (tt) REVERT: H 105 GLU cc_start: 0.7990 (tp30) cc_final: 0.7756 (tp30) REVERT: M 19 ASN cc_start: 0.9375 (t0) cc_final: 0.9168 (t0) REVERT: M 28 TRP cc_start: 0.8117 (t60) cc_final: 0.7911 (t60) REVERT: M 51 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: M 74 MET cc_start: 0.8732 (tpp) cc_final: 0.8381 (tpp) REVERT: M 79 HIS cc_start: 0.8447 (p-80) cc_final: 0.7925 (m90) REVERT: M 88 MET cc_start: 0.5760 (ttm) cc_final: 0.5221 (tmm) REVERT: M 151 TYR cc_start: 0.8231 (m-10) cc_final: 0.7745 (m-10) REVERT: M 162 PHE cc_start: 0.8780 (m-80) cc_final: 0.8572 (m-80) REVERT: M 171 ASN cc_start: 0.7689 (t160) cc_final: 0.6842 (t0) outliers start: 23 outliers final: 16 residues processed: 228 average time/residue: 0.2889 time to fit residues: 91.3605 Evaluate side-chains 213 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 23 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4609 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= 0.169 Angle : 0.578 9.602 21353 Z= 0.338 Chirality : 0.035 0.160 2418 Planarity : 0.004 0.045 1677 Dihedral : 29.710 141.441 4412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.25 % Allowed : 21.93 % Favored : 74.82 % 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: -2.26 (0.26), residues: 979 helix: -1.03 (0.21), residues: 561 sheet: 0.56 (1.00), residues: 26 loop : -2.24 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 531 HIS 0.010 0.001 HIS D 82 PHE 0.017 0.001 PHE B 100 TYR 0.024 0.001 TYR E 110 ARG 0.008 0.001 ARG B 95 *********************** 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 225 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6126 (mmt-90) cc_final: 0.4940 (mmm-85) REVERT: C 24 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8027 (mp10) REVERT: C 39 TYR cc_start: 0.8394 (m-80) cc_final: 0.8144 (m-80) REVERT: C 41 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7479 (tt0) REVERT: C 56 GLU cc_start: 0.7341 (tt0) cc_final: 0.6544 (tt0) REVERT: D 52 THR cc_start: 0.9108 (m) cc_final: 0.8745 (p) REVERT: D 86 ARG cc_start: 0.6902 (mpt-90) cc_final: 0.6023 (mtp180) REVERT: E 80 ARG cc_start: 0.8653 (pmt170) cc_final: 0.7369 (mmt90) REVERT: E 96 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8224 (mm-30) REVERT: E 122 PHE cc_start: 0.7245 (m-80) cc_final: 0.6893 (m-10) REVERT: F 44 LYS cc_start: 0.7434 (tttt) cc_final: 0.7021 (tptm) REVERT: F 84 MET cc_start: 0.7064 (tpt) cc_final: 0.6391 (mmt) REVERT: F 92 ARG cc_start: 0.7648 (tmm-80) cc_final: 0.7251 (tmm-80) REVERT: F 97 LEU cc_start: 0.7888 (tp) cc_final: 0.7556 (tp) REVERT: G 36 LYS cc_start: 0.7653 (mmpt) cc_final: 0.7242 (tmtt) REVERT: G 38 ASN cc_start: 0.9066 (m-40) cc_final: 0.8590 (p0) REVERT: G 51 LEU cc_start: 0.7488 (tp) cc_final: 0.7235 (tt) REVERT: H 105 GLU cc_start: 0.8043 (tp30) cc_final: 0.7765 (tp30) REVERT: M 1 MET cc_start: 0.0775 (mpp) cc_final: -0.0852 (tpt) REVERT: M 28 TRP cc_start: 0.8134 (t60) cc_final: 0.7842 (t60) REVERT: M 74 MET cc_start: 0.8730 (tpp) cc_final: 0.8375 (tpp) REVERT: M 79 HIS cc_start: 0.8398 (p-80) cc_final: 0.7916 (m90) REVERT: M 88 MET cc_start: 0.5702 (ttm) cc_final: 0.5129 (tmm) REVERT: M 101 MET cc_start: 0.6746 (ptp) cc_final: 0.6329 (mpp) REVERT: M 131 VAL cc_start: 0.7794 (p) cc_final: 0.7513 (m) REVERT: M 162 PHE cc_start: 0.8795 (m-80) cc_final: 0.8563 (m-80) REVERT: M 171 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7337 (t0) outliers start: 27 outliers final: 20 residues processed: 208 average time/residue: 0.2663 time to fit residues: 79.2063 Evaluate side-chains 210 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 THR 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 41 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR 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 107 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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** C 84 GLN D 82 HIS 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 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14874 Z= 0.329 Angle : 0.688 10.604 21353 Z= 0.388 Chirality : 0.040 0.165 2418 Planarity : 0.004 0.051 1677 Dihedral : 29.754 135.730 4412 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.02 % Allowed : 21.45 % 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: -2.41 (0.26), residues: 979 helix: -1.17 (0.21), residues: 566 sheet: 0.60 (1.01), residues: 27 loop : -2.31 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 531 HIS 0.011 0.002 HIS D 82 PHE 0.016 0.002 PHE A 67 TYR 0.026 0.002 TYR E 110 ARG 0.004 0.001 ARG F 95 *********************** 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 248 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6410 (mmt-90) cc_final: 0.5622 (mmm-85) REVERT: A 92 LEU cc_start: 0.7708 (mt) cc_final: 0.6941 (tt) REVERT: A 110 TYR cc_start: 0.7707 (t80) cc_final: 0.7436 (t80) REVERT: B 29 ILE cc_start: 0.8008 (mm) cc_final: 0.7532 (mm) REVERT: C 41 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7820 (tt0) REVERT: C 56 GLU cc_start: 0.7500 (tt0) cc_final: 0.6766 (tt0) REVERT: C 90 ASP cc_start: 0.7106 (t70) cc_final: 0.6699 (t0) REVERT: D 52 THR cc_start: 0.9099 (m) cc_final: 0.8642 (p) REVERT: D 86 ARG cc_start: 0.7344 (mpt-90) cc_final: 0.6546 (mtp180) REVERT: E 65 LEU cc_start: 0.8056 (tp) cc_final: 0.7807 (tt) REVERT: E 80 ARG cc_start: 0.8648 (pmt170) cc_final: 0.7438 (mmt90) REVERT: E 122 PHE cc_start: 0.7336 (m-80) cc_final: 0.7071 (m-80) REVERT: F 84 MET cc_start: 0.7344 (tpt) cc_final: 0.6753 (mmt) REVERT: F 92 ARG cc_start: 0.7700 (tmm-80) cc_final: 0.7190 (tmm-80) REVERT: G 36 LYS cc_start: 0.7815 (mmpt) cc_final: 0.7364 (tmtt) REVERT: G 38 ASN cc_start: 0.9017 (m-40) cc_final: 0.8714 (t0) REVERT: G 41 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7952 (tm-30) REVERT: G 99 ARG cc_start: 0.8420 (mmt90) cc_final: 0.7059 (mtm180) REVERT: H 93 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7683 (mt-10) REVERT: M 1 MET cc_start: 0.1520 (mpp) cc_final: 0.1190 (mmt) REVERT: M 28 TRP cc_start: 0.8299 (t60) cc_final: 0.7968 (t60) REVERT: M 74 MET cc_start: 0.8750 (tpp) cc_final: 0.8322 (tpp) REVERT: M 79 HIS cc_start: 0.8467 (p-80) cc_final: 0.7964 (m90) REVERT: M 88 MET cc_start: 0.5707 (ttm) cc_final: 0.5394 (tmm) REVERT: M 131 VAL cc_start: 0.7875 (p) cc_final: 0.7586 (m) REVERT: M 162 PHE cc_start: 0.8831 (m-80) cc_final: 0.8578 (m-80) REVERT: M 171 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7266 (t0) outliers start: 50 outliers final: 39 residues processed: 221 average time/residue: 0.2734 time to fit residues: 85.6926 Evaluate side-chains 228 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 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 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL 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 101 LEU 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 37 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4919 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= 0.210 Angle : 0.608 10.546 21353 Z= 0.351 Chirality : 0.036 0.174 2418 Planarity : 0.004 0.056 1677 Dihedral : 29.681 139.021 4412 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.94 % Allowed : 23.86 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -2.07 (0.26), residues: 979 helix: -0.87 (0.21), residues: 565 sheet: 0.79 (1.03), residues: 27 loop : -2.22 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 137 HIS 0.006 0.001 HIS B 75 PHE 0.018 0.001 PHE B 100 TYR 0.028 0.002 TYR D 40 ARG 0.010 0.000 ARG A 131 *********************** 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 230 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6413 (mmt-90) cc_final: 0.5581 (mmm-85) REVERT: A 139 LEU cc_start: 0.6891 (tt) cc_final: 0.6537 (tt) REVERT: B 37 LEU cc_start: 0.7951 (tp) cc_final: 0.7741 (tp) REVERT: C 41 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7592 (tt0) REVERT: C 56 GLU cc_start: 0.7413 (tt0) cc_final: 0.6700 (tt0) REVERT: D 86 ARG cc_start: 0.7243 (mpt-90) cc_final: 0.6438 (mtp180) REVERT: E 80 ARG cc_start: 0.8567 (pmt170) cc_final: 0.7366 (mmt90) REVERT: E 104 HIS cc_start: 0.7719 (t-90) cc_final: 0.7363 (t70) REVERT: E 122 PHE cc_start: 0.7186 (m-80) cc_final: 0.6801 (m-10) REVERT: F 44 LYS cc_start: 0.7574 (tptt) cc_final: 0.7299 (tptm) REVERT: F 84 MET cc_start: 0.7202 (tpt) cc_final: 0.6471 (mmt) REVERT: F 92 ARG cc_start: 0.7850 (tmm-80) cc_final: 0.7452 (tmm-80) REVERT: G 36 LYS cc_start: 0.7718 (mmpt) cc_final: 0.7265 (tmtt) REVERT: G 38 ASN cc_start: 0.9023 (m-40) cc_final: 0.8679 (p0) REVERT: G 41 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7956 (tm-30) REVERT: M 1 MET cc_start: 0.1560 (mpp) cc_final: 0.1194 (mmt) REVERT: M 28 TRP cc_start: 0.8313 (t60) cc_final: 0.7958 (t60) REVERT: M 74 MET cc_start: 0.8719 (tpp) cc_final: 0.8296 (tpp) REVERT: M 79 HIS cc_start: 0.8373 (p-80) cc_final: 0.8096 (m90) REVERT: M 82 VAL cc_start: 0.6053 (t) cc_final: 0.5829 (t) REVERT: M 88 MET cc_start: 0.5882 (ttm) cc_final: 0.5513 (tmm) REVERT: M 131 VAL cc_start: 0.7987 (p) cc_final: 0.7723 (m) REVERT: M 162 PHE cc_start: 0.8749 (m-80) cc_final: 0.8498 (m-80) REVERT: M 171 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7214 (t0) outliers start: 41 outliers final: 33 residues processed: 209 average time/residue: 0.2574 time to fit residues: 77.3663 Evaluate side-chains 219 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 ARG 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 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 59 HIS E 95 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5211 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= 0.183 Angle : 0.592 11.014 21353 Z= 0.341 Chirality : 0.036 0.158 2418 Planarity : 0.004 0.051 1677 Dihedral : 29.625 138.941 4412 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.10 % Allowed : 25.06 % Favored : 70.84 % 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: -1.82 (0.26), residues: 979 helix: -0.60 (0.22), residues: 570 sheet: 0.78 (0.97), residues: 27 loop : -2.23 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 530 HIS 0.010 0.001 HIS D 82 PHE 0.015 0.001 PHE B 100 TYR 0.021 0.001 TYR E 110 ARG 0.010 0.000 ARG A 131 *********************** 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 226 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.6085 (mmt-90) cc_final: 0.5171 (mmm-85) REVERT: A 80 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6261 (mtm180) REVERT: A 99 GLU cc_start: 0.7344 (tp30) cc_final: 0.6921 (tm-30) REVERT: A 139 LEU cc_start: 0.7210 (tt) cc_final: 0.6771 (tt) REVERT: B 29 ILE cc_start: 0.7971 (mm) cc_final: 0.7422 (mm) REVERT: B 47 SER cc_start: 0.8931 (t) cc_final: 0.8532 (m) REVERT: C 41 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7499 (tt0) REVERT: C 56 GLU cc_start: 0.7410 (tt0) cc_final: 0.6901 (tt0) REVERT: D 86 ARG cc_start: 0.7055 (mpt-90) cc_final: 0.6202 (mtp180) REVERT: E 80 ARG cc_start: 0.8595 (pmt170) cc_final: 0.8348 (pmt-80) REVERT: E 122 PHE cc_start: 0.7185 (m-80) cc_final: 0.6760 (m-10) REVERT: F 44 LYS cc_start: 0.7505 (tptt) cc_final: 0.7222 (tptm) REVERT: F 84 MET cc_start: 0.7184 (tpt) cc_final: 0.6457 (mmt) REVERT: F 92 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7529 (tmm-80) REVERT: G 36 LYS cc_start: 0.7664 (mmpt) cc_final: 0.7224 (tmtt) REVERT: G 38 ASN cc_start: 0.9020 (m-40) cc_final: 0.8708 (p0) REVERT: G 41 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7907 (tm-30) REVERT: K 525 ARG cc_start: 0.6392 (mtt-85) cc_final: 0.5834 (mtm-85) REVERT: M 3 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7861 (tm-30) REVERT: M 28 TRP cc_start: 0.8344 (t60) cc_final: 0.7975 (t60) REVERT: M 74 MET cc_start: 0.8714 (tpp) cc_final: 0.8317 (tpp) REVERT: M 79 HIS cc_start: 0.8384 (p-80) cc_final: 0.8008 (m90) REVERT: M 82 VAL cc_start: 0.6071 (t) cc_final: 0.5842 (t) REVERT: M 101 MET cc_start: 0.6791 (pmm) cc_final: 0.6224 (pmm) REVERT: M 131 VAL cc_start: 0.8015 (p) cc_final: 0.7759 (m) REVERT: M 162 PHE cc_start: 0.8779 (m-80) cc_final: 0.8500 (m-80) REVERT: M 171 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7139 (t0) outliers start: 34 outliers final: 27 residues processed: 207 average time/residue: 0.2568 time to fit residues: 76.6916 Evaluate side-chains 213 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 THR 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 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 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 F residue 70 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR 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 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 103 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5483 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= 0.171 Angle : 0.585 11.865 21353 Z= 0.336 Chirality : 0.035 0.155 2418 Planarity : 0.004 0.044 1677 Dihedral : 29.572 139.978 4412 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.98 % Allowed : 25.06 % Favored : 70.96 % 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: -1.55 (0.26), residues: 979 helix: -0.33 (0.22), residues: 574 sheet: 1.27 (1.02), residues: 27 loop : -2.26 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 530 HIS 0.009 0.001 HIS M 185 PHE 0.016 0.001 PHE M 8 TYR 0.019 0.001 TYR E 110 ARG 0.010 0.000 ARG A 131 *********************** 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 232 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6238 (mtm180) REVERT: A 99 GLU cc_start: 0.7542 (tp30) cc_final: 0.6928 (tm-30) REVERT: B 47 SER cc_start: 0.8893 (t) cc_final: 0.8474 (m) REVERT: C 41 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7617 (tt0) REVERT: C 56 GLU cc_start: 0.7463 (tt0) cc_final: 0.6935 (tt0) REVERT: D 86 ARG cc_start: 0.7014 (mpt-90) cc_final: 0.6169 (mtp180) REVERT: E 80 ARG cc_start: 0.8612 (pmt170) cc_final: 0.8387 (pmt-80) REVERT: E 95 GLN cc_start: 0.7896 (tt0) cc_final: 0.7436 (mm-40) REVERT: E 96 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7850 (mm-30) REVERT: E 122 PHE cc_start: 0.7204 (m-80) cc_final: 0.6709 (m-10) REVERT: F 84 MET cc_start: 0.7110 (tpt) cc_final: 0.6388 (mmt) REVERT: F 92 ARG cc_start: 0.7900 (tmm-80) cc_final: 0.7438 (tmm-80) REVERT: G 36 LYS cc_start: 0.7668 (mmpt) cc_final: 0.7237 (tmtt) REVERT: G 38 ASN cc_start: 0.9009 (m-40) cc_final: 0.8732 (p0) REVERT: G 41 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7795 (tm-30) REVERT: M 3 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7937 (tm-30) REVERT: M 28 TRP cc_start: 0.8323 (t60) cc_final: 0.7988 (t60) REVERT: M 74 MET cc_start: 0.8699 (tpp) cc_final: 0.8326 (tpp) REVERT: M 79 HIS cc_start: 0.8346 (p-80) cc_final: 0.7974 (m90) REVERT: M 82 VAL cc_start: 0.6076 (t) cc_final: 0.5841 (t) REVERT: M 101 MET cc_start: 0.6289 (pmm) cc_final: 0.6079 (pmm) REVERT: M 131 VAL cc_start: 0.8026 (p) cc_final: 0.7761 (m) REVERT: M 162 PHE cc_start: 0.8727 (m-80) cc_final: 0.8495 (m-80) REVERT: M 171 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7155 (t0) outliers start: 33 outliers final: 28 residues processed: 216 average time/residue: 0.2428 time to fit residues: 76.5910 Evaluate side-chains 219 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 70 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 37 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 G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14874 Z= 0.227 Angle : 0.626 11.876 21353 Z= 0.353 Chirality : 0.037 0.152 2418 Planarity : 0.004 0.047 1677 Dihedral : 29.609 136.983 4412 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.73 % Allowed : 25.30 % Favored : 70.96 % 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: -1.51 (0.27), residues: 979 helix: -0.30 (0.22), residues: 572 sheet: 1.05 (0.99), residues: 27 loop : -2.22 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 530 HIS 0.006 0.001 HIS M 185 PHE 0.018 0.001 PHE M 8 TYR 0.015 0.001 TYR E 110 ARG 0.010 0.001 ARG A 131 ********************** 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 222 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6351 (mtm180) REVERT: A 110 TYR cc_start: 0.7837 (t80) cc_final: 0.7600 (t80) REVERT: C 41 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7557 (tt0) REVERT: C 56 GLU cc_start: 0.7537 (tt0) cc_final: 0.6803 (tt0) REVERT: C 90 ASP cc_start: 0.6685 (t70) cc_final: 0.6341 (t0) REVERT: D 86 ARG cc_start: 0.7116 (mpt-90) cc_final: 0.6293 (mtp180) REVERT: E 80 ARG cc_start: 0.8635 (pmt170) cc_final: 0.8366 (pmt-80) REVERT: E 122 PHE cc_start: 0.7284 (m-80) cc_final: 0.6782 (m-10) REVERT: F 44 LYS cc_start: 0.7645 (tptm) cc_final: 0.7311 (mmmm) REVERT: F 47 SER cc_start: 0.8909 (t) cc_final: 0.8112 (m) REVERT: F 92 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7448 (tmm-80) REVERT: F 98 TYR cc_start: 0.7566 (m-10) cc_final: 0.7344 (m-80) REVERT: G 36 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7281 (tmtt) REVERT: G 38 ASN cc_start: 0.9021 (m-40) cc_final: 0.8717 (p0) REVERT: G 41 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7901 (tm-30) REVERT: M 3 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7954 (tm-30) REVERT: M 28 TRP cc_start: 0.8345 (t60) cc_final: 0.7977 (t60) REVERT: M 74 MET cc_start: 0.8709 (tpp) cc_final: 0.8324 (tpp) REVERT: M 79 HIS cc_start: 0.8357 (p-80) cc_final: 0.7977 (m90) REVERT: M 82 VAL cc_start: 0.6174 (t) cc_final: 0.5942 (t) REVERT: M 131 VAL cc_start: 0.8093 (p) cc_final: 0.7843 (m) REVERT: M 162 PHE cc_start: 0.8765 (m-80) cc_final: 0.8514 (m-80) REVERT: M 171 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7316 (t0) outliers start: 31 outliers final: 28 residues processed: 206 average time/residue: 0.2511 time to fit residues: 74.9443 Evaluate side-chains 215 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 37 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 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 101 THR Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 90 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.4059 r_free = 0.4059 target = 0.153187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090941 restraints weight = 23860.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094246 restraints weight = 11961.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096385 restraints weight = 8084.059| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5651 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= 0.207 Angle : 0.616 12.230 21353 Z= 0.349 Chirality : 0.036 0.176 2418 Planarity : 0.004 0.078 1677 Dihedral : 29.612 137.897 4412 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.61 % Allowed : 25.90 % Favored : 70.48 % 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: -1.32 (0.27), residues: 979 helix: -0.16 (0.22), residues: 572 sheet: 1.32 (1.00), residues: 27 loop : -2.13 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 530 HIS 0.012 0.001 HIS D 82 PHE 0.019 0.001 PHE B 100 TYR 0.017 0.001 TYR M 73 ARG 0.010 0.000 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.29 seconds wall clock time: 45 minutes 53.01 seconds (2753.01 seconds total)