Starting phenix.real_space_refine (version: dev) on Wed Apr 6 18:51:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/04_2022/7tao_25779_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.231 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ASP 121": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 22497 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1144 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1472 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2801 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 7, 'TRANS': 335, 'PCIS': 2} Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6089 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'WEV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.24, per 1000 atoms: 0.63 Number of scatterers: 22497 At special positions: 0 Unit cell: (124.324, 119.496, 133.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4020 8.00 N 3542 7.00 C 14800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 75 " distance=2.02 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: 9.31 Conformation dependent library (CDL) restraints added in 3.5 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 3 sheets defined 73.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'D' and resid 15 through 51 removed outlier: 3.786A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 61 through 83 removed outlier: 3.910A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 127 removed outlier: 3.949A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 163 removed outlier: 4.263A pdb=" N VAL D 135 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 146 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 147 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 163 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 56 through 90 removed outlier: 3.545A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 124 removed outlier: 3.502A pdb=" N THR C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR C 98 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 101 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 102 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 109 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 110 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 removed outlier: 3.790A pdb=" N ALA C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 205 removed outlier: 3.515A pdb=" N PHE C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 182 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 185 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 186 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 Processing helix chain 'N' and resid 252 through 254 No H-bonds generated for 'chain 'N' and resid 252 through 254' Processing helix chain 'M' and resid 4 through 24 Processing helix chain 'M' and resid 30 through 55 removed outlier: 3.567A pdb=" N GLN M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.566A pdb=" N PHE E 23 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL E 37 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS E 43 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.868A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 118 Processing helix chain 'E' and resid 123 through 153 removed outlier: 3.790A pdb=" N VAL E 127 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 32 Processing helix chain 'O' and resid 36 through 39 No H-bonds generated for 'chain 'O' and resid 36 through 39' Processing helix chain 'O' and resid 48 through 74 Processing helix chain 'F' and resid 7 through 42 Proline residue: F 10 - end of helix removed outlier: 3.858A pdb=" N ALA F 20 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR F 24 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 35 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.694A pdb=" N PHE F 51 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE F 54 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL F 55 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Proline residue: F 56 - end of helix removed outlier: 3.518A pdb=" N MET F 59 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS F 75 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 119 removed outlier: 3.711A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 153 removed outlier: 3.642A pdb=" N PHE F 126 " --> pdb=" O PRO F 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 127 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 45 removed outlier: 3.725A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 75 Proline residue: G 56 - end of helix removed outlier: 3.561A pdb=" N ILE G 63 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS G 75 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 117 removed outlier: 3.787A pdb=" N ALA G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 123 through 152 removed outlier: 3.548A pdb=" N GLU G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 138 " --> pdb=" O PHE G 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 45 removed outlier: 3.749A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 77 removed outlier: 3.637A pdb=" N ILE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 121 removed outlier: 4.679A pdb=" N GLY H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 153 removed outlier: 3.701A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG H 153 " --> pdb=" O LEU H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 43 Proline residue: I 10 - end of helix removed outlier: 3.739A pdb=" N SER I 19 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 20 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR I 24 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL I 37 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS I 43 " --> pdb=" O CYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 52 through 77 removed outlier: 3.626A pdb=" N VAL I 55 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Proline residue: I 56 - end of helix Processing helix chain 'I' and resid 84 through 121 removed outlier: 4.089A pdb=" N ALA I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 154 Processing helix chain 'J' and resid 7 through 42 Proline residue: J 10 - end of helix removed outlier: 3.636A pdb=" N ALA J 20 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE J 23 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR J 24 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER J 35 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 55 through 77 removed outlier: 3.850A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 118 removed outlier: 3.687A pdb=" N ALA J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 152 removed outlier: 3.758A pdb=" N VAL J 138 " --> pdb=" O PHE J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 42 removed outlier: 3.654A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 55 through 75 removed outlier: 3.801A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.698A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 153 removed outlier: 3.587A pdb=" N VAL K 127 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL K 138 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 43 removed outlier: 3.721A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 53 through 77 Proline residue: L 56 - end of helix Processing helix chain 'L' and resid 84 through 121 removed outlier: 3.708A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 153 removed outlier: 3.888A pdb=" N VAL L 127 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL L 138 " --> pdb=" O PHE L 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 No H-bonds generated for 'chain 'B' and resid 6 through 9' Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.574A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 116 removed outlier: 3.712A pdb=" N GLY B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 204 through 228 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 262 through 271 removed outlier: 4.489A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.525A pdb=" N LYS B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 332 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'A' and resid 23 through 36 removed outlier: 5.684A pdb=" N ARG A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 36 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 104 through 145 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 193 through 207 removed outlier: 4.680A pdb=" N ALA A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 280 through 303 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 360 removed outlier: 4.366A pdb=" N ALA A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.769A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.704A pdb=" N ILE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.670A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 526 through 562 removed outlier: 4.466A pdb=" N LEU A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 533 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 543 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 546 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.812A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 Proline residue: A 646 - end of helix removed outlier: 5.136A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 754 removed outlier: 3.914A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.235A pdb=" N GLY A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 763 through 784 Processing helix chain 'A' and resid 789 through 802 removed outlier: 3.678A pdb=" N MET A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 809 No H-bonds generated for 'chain 'A' and resid 806 through 809' Processing sheet with id= A, first strand: chain 'A' and resid 334 through 342 removed outlier: 3.802A pdb=" N ILE A 341 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 removed outlier: 3.521A pdb=" N GLU A 229 " --> pdb=" O ASP A 224 " (cutoff:3.500A) 1613 hydrogen bonds defined for protein. 3321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3491 1.32 - 1.45: 6118 1.45 - 1.57: 13117 1.57 - 1.70: 24 1.70 - 1.83: 204 Bond restraints: 22954 Sorted by residual: bond pdb=" C26 WEV K 901 " pdb=" O41 WEV K 901 " ideal model delta sigma weight residual 0.000 1.381 -1.381 2.00e-02 2.50e+03 4.77e+03 bond pdb=" C26 WEV F 201 " pdb=" O41 WEV F 201 " ideal model delta sigma weight residual 0.000 1.380 -1.380 2.00e-02 2.50e+03 4.76e+03 bond pdb=" C26 WEV E 201 " pdb=" O41 WEV E 201 " ideal model delta sigma weight residual 0.000 1.380 -1.380 2.00e-02 2.50e+03 4.76e+03 bond pdb=" C26 WEV G 201 " pdb=" O41 WEV G 201 " ideal model delta sigma weight residual 0.000 1.380 -1.380 2.00e-02 2.50e+03 4.76e+03 bond pdb=" C26 WEV I 201 " pdb=" O41 WEV I 201 " ideal model delta sigma weight residual 0.000 1.378 -1.378 2.00e-02 2.50e+03 4.75e+03 ... (remaining 22949 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.28: 417 106.28 - 113.21: 12811 113.21 - 120.14: 8164 120.14 - 127.08: 9643 127.08 - 134.01: 170 Bond angle restraints: 31205 Sorted by residual: angle pdb=" C02 WEV E 201 " pdb=" C03 WEV E 201 " pdb=" C04 WEV E 201 " ideal model delta sigma weight residual 5.19 120.96 -115.77 3.00e+00 1.11e-01 1.49e+03 angle pdb=" C02 WEV F 201 " pdb=" C03 WEV F 201 " pdb=" C04 WEV F 201 " ideal model delta sigma weight residual 5.19 115.82 -110.63 3.00e+00 1.11e-01 1.36e+03 angle pdb=" C02 WEV H 201 " pdb=" C03 WEV H 201 " pdb=" C04 WEV H 201 " ideal model delta sigma weight residual 5.19 115.52 -110.33 3.00e+00 1.11e-01 1.35e+03 angle pdb=" C02 WEV D 202 " pdb=" C03 WEV D 202 " pdb=" C04 WEV D 202 " ideal model delta sigma weight residual 5.19 115.07 -109.88 3.00e+00 1.11e-01 1.34e+03 angle pdb=" C02 WEV J 201 " pdb=" C03 WEV J 201 " pdb=" C04 WEV J 201 " ideal model delta sigma weight residual 5.19 114.66 -109.47 3.00e+00 1.11e-01 1.33e+03 ... (remaining 31200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 12905 35.86 - 71.72: 205 71.72 - 107.58: 28 107.58 - 143.44: 12 143.44 - 179.30: 5 Dihedral angle restraints: 13155 sinusoidal: 4881 harmonic: 8274 Sorted by residual: dihedral pdb=" C09 WEV D 201 " pdb=" C11 WEV D 201 " pdb=" O10 WEV D 201 " pdb=" C13 WEV D 201 " ideal model delta sinusoidal sigma weight residual -115.82 63.48 -179.30 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C09 WEV D 202 " pdb=" C11 WEV D 202 " pdb=" O10 WEV D 202 " pdb=" C13 WEV D 202 " ideal model delta sinusoidal sigma weight residual -115.82 62.41 -178.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C02 WEV E 201 " pdb=" C03 WEV E 201 " pdb=" C04 WEV E 201 " pdb=" C05 WEV E 201 " ideal model delta sinusoidal sigma weight residual -104.90 55.95 -160.85 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 13152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3690 0.153 - 0.305: 18 0.305 - 0.458: 11 0.458 - 0.610: 14 0.610 - 0.763: 13 Chirality restraints: 3746 Sorted by residual: chirality pdb=" C24 WEV I 201 " pdb=" C09 WEV I 201 " pdb=" C25 WEV I 201 " pdb=" C26 WEV I 201 " both_signs ideal model delta sigma weight residual False -3.31 -2.55 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C08 WEV K 901 " pdb=" C07 WEV K 901 " pdb=" C09 WEV K 901 " pdb=" O42 WEV K 901 " both_signs ideal model delta sigma weight residual False -1.87 -2.56 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C24 WEV D 201 " pdb=" C09 WEV D 201 " pdb=" C25 WEV D 201 " pdb=" C26 WEV D 201 " both_signs ideal model delta sigma weight residual False -3.31 -2.64 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 3743 not shown) Planarity restraints: 3841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 618 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 619 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 77 " -0.012 2.00e-02 2.50e+03 1.15e-02 3.28e+00 pdb=" CG TRP C 77 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 77 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 77 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN N 259 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO N 260 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO N 260 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 260 " 0.022 5.00e-02 4.00e+02 ... (remaining 3838 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 250 2.67 - 3.23: 23040 3.23 - 3.78: 37896 3.78 - 4.34: 51315 4.34 - 4.90: 84422 Nonbonded interactions: 196923 Sorted by model distance: nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.109 2.440 nonbonded pdb=" ND2 ASN A 480 " pdb=" O LEU A 518 " model vdw 2.145 2.520 nonbonded pdb=" OH TYR H 142 " pdb=" O19 WEV H 201 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR J 142 " pdb=" O19 WEV J 201 " model vdw 2.177 2.440 nonbonded pdb=" ND2 ASN B 106 " pdb=" O HIS B 128 " model vdw 2.186 2.520 ... (remaining 196918 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14800 2.51 5 N 3542 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 5.820 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.180 Process input model: 58.810 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.057 1.381 22954 Z= 3.825 Angle : 3.163 115.767 31205 Z= 1.076 Chirality : 0.068 0.763 3746 Planarity : 0.004 0.064 3841 Dihedral : 15.767 179.297 7900 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 2881 helix: 1.89 (0.11), residues: 2140 sheet: -0.80 (1.01), residues: 29 loop : -0.34 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.438 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3375 time to fit residues: 152.0610 Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN B 209 GLN A 134 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.223 22954 Z= 0.509 Angle : 1.976 47.206 31205 Z= 0.710 Chirality : 0.067 1.387 3746 Planarity : 0.009 0.108 3841 Dihedral : 13.681 170.484 3155 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.21 (0.15), residues: 2881 helix: 1.23 (0.11), residues: 2145 sheet: -0.83 (0.98), residues: 29 loop : -0.26 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 2.363 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 261 average time/residue: 0.3401 time to fit residues: 139.1098 Evaluate side-chains 257 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2153 time to fit residues: 7.7792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.330 22954 Z= 0.850 Angle : 2.003 50.003 31205 Z= 0.740 Chirality : 0.067 1.387 3746 Planarity : 0.009 0.108 3841 Dihedral : 13.681 170.485 3155 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.21 (0.15), residues: 2881 helix: 1.23 (0.11), residues: 2145 sheet: -0.83 (0.98), residues: 29 loop : -0.26 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3525 time to fit residues: 137.5291 Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 0.0980 chunk 192 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 256 optimal weight: 0.6980 chunk 271 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 243 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.258 22954 Z= 0.820 Angle : 2.040 57.688 31205 Z= 0.750 Chirality : 0.067 1.383 3746 Planarity : 0.009 0.108 3841 Dihedral : 13.679 170.534 3155 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.20 (0.15), residues: 2881 helix: 1.23 (0.11), residues: 2145 sheet: -0.83 (0.98), residues: 29 loop : -0.26 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3559 time to fit residues: 136.2159 Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 112 optimal weight: 0.0050 chunk 231 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.334 22954 Z= 0.515 Angle : 1.789 44.823 31205 Z= 0.651 Chirality : 0.058 0.887 3746 Planarity : 0.008 0.084 3841 Dihedral : 13.512 179.671 3155 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.92 (0.15), residues: 2881 helix: 0.99 (0.11), residues: 2145 sheet: -0.77 (1.00), residues: 29 loop : -0.24 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 249 time to evaluate : 2.626 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 251 average time/residue: 0.3583 time to fit residues: 140.2888 Evaluate side-chains 250 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2014 time to fit residues: 4.8737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 142 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.105 22954 Z= 0.759 Angle : 1.832 47.065 31205 Z= 0.681 Chirality : 0.058 0.887 3746 Planarity : 0.008 0.084 3841 Dihedral : 13.514 179.703 3155 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.92 (0.15), residues: 2881 helix: 0.99 (0.11), residues: 2145 sheet: -0.77 (1.00), residues: 29 loop : -0.24 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.363 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 246 average time/residue: 0.3662 time to fit residues: 140.1697 Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.493 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2060 time to fit residues: 3.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 228 optimal weight: 0.0370 chunk 151 optimal weight: 0.8980 chunk 270 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.509 22954 Z= 0.525 Angle : 1.748 42.813 31205 Z= 0.636 Chirality : 0.058 0.892 3746 Planarity : 0.007 0.096 3841 Dihedral : 13.638 177.625 3155 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.91 (0.15), residues: 2881 helix: 0.98 (0.11), residues: 2145 sheet: -0.73 (1.00), residues: 29 loop : -0.25 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 2.435 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 246 average time/residue: 0.3534 time to fit residues: 135.5925 Evaluate side-chains 248 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2187 time to fit residues: 5.3283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 0.0040 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.509 22954 Z= 0.525 Angle : 1.747 42.813 31205 Z= 0.636 Chirality : 0.058 0.892 3746 Planarity : 0.007 0.096 3841 Dihedral : 13.638 177.625 3155 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.91 (0.15), residues: 2881 helix: 0.98 (0.11), residues: 2145 sheet: -0.73 (1.00), residues: 29 loop : -0.25 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3676 time to fit residues: 140.7131 Evaluate side-chains 244 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 198 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 0.3980 chunk 238 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.202 22954 Z= 0.470 Angle : 1.709 41.707 31205 Z= 0.621 Chirality : 0.058 0.863 3746 Planarity : 0.007 0.095 3841 Dihedral : 13.671 175.586 3155 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.89 (0.15), residues: 2881 helix: 0.96 (0.11), residues: 2145 sheet: -0.71 (1.01), residues: 29 loop : -0.25 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.618 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 247 average time/residue: 0.3555 time to fit residues: 137.4509 Evaluate side-chains 247 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 2.286 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2021 time to fit residues: 5.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.0010 chunk 266 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 279 optimal weight: 0.0040 chunk 257 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.201 22954 Z= 0.470 Angle : 1.709 41.706 31205 Z= 0.621 Chirality : 0.058 0.863 3746 Planarity : 0.007 0.095 3841 Dihedral : 13.671 175.584 3155 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.89 (0.15), residues: 2881 helix: 0.96 (0.11), residues: 2145 sheet: -0.71 (1.01), residues: 29 loop : -0.25 (0.24), residues: 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3702 time to fit residues: 140.6826 Evaluate side-chains 243 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.9990 chunk 237 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 223 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124353 restraints weight = 34888.907| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.11 r_work: 0.3298 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.1250 r_work: 0.3166 rms_B_bonded: 2.98 restraints_weight: 0.0625 r_work: 0.3081 rms_B_bonded: 4.12 restraints_weight: 0.0312 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.201 22954 Z= 0.470 Angle : 1.709 41.706 31205 Z= 0.621 Chirality : 0.058 0.863 3746 Planarity : 0.007 0.095 3841 Dihedral : 13.671 175.584 3155 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.89 (0.15), residues: 2881 helix: 0.96 (0.11), residues: 2145 sheet: -0.71 (1.01), residues: 29 loop : -0.25 (0.24), residues: 707 =============================================================================== Job complete usr+sys time: 3588.45 seconds wall clock time: 67 minutes 17.69 seconds (4037.69 seconds total)