Starting phenix.real_space_refine (version: dev) on Sun Feb 19 18:03:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2023/8f6j_28885.pdb" } resolution = 3.7 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= 0.018 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 Process input model Symmetric amino acids flipped Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.01, per 1000 atoms: 0.57 Number of scatterers: 10472 At special positions: 0 Unit cell: (67.977, 156.455, 145.665, 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) Zn 8 29.99 S 28 16.00 O 2000 8.00 N 1760 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 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: 4.03 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 77 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 73 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS A 285 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 33.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.510A pdb=" N ARG B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 67 removed outlier: 3.721A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 4.484A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 142 removed outlier: 3.807A pdb=" N VAL B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.632A pdb=" N VAL B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.791A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 208 removed outlier: 4.101A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.595A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.568A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'F' and resid 90 through 94 removed outlier: 4.085A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.522A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.561A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 103 removed outlier: 4.470A pdb=" N ALA A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 95 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.958A pdb=" N ASN A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 141 removed outlier: 3.783A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.564A pdb=" N VAL A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.887A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 208 removed outlier: 4.220A pdb=" N ASP A 181 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.593A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.567A pdb=" N ILE A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.305A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.517A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 4.076A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.365A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 249 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.807A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.053A pdb=" N ILE E 92 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR E 99 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 94 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 116 through 120 removed outlier: 3.644A pdb=" N SER E 116 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 178 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.675A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 61 through 63 removed outlier: 5.649A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AB1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.694A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.367A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 250 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB6, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.801A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.052A pdb=" N ILE C 92 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR C 99 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 94 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.661A pdb=" N SER C 116 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 178 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.519A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 21 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 63 removed outlier: 5.645A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.683A pdb=" N THR D 168 " --> pdb=" O ASN D 216 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1296 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: 2.85 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3344 1.34 - 1.46: 2301 1.46 - 1.58: 5009 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10692 Sorted by residual: bond pdb=" CB PRO F 184 " pdb=" CG PRO F 184 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" CB PRO D 184 " pdb=" CG PRO D 184 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.29e+00 bond pdb=" CG PRO F 184 " pdb=" CD PRO F 184 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.23e+00 bond pdb=" CB PRO E 81 " pdb=" CG PRO E 81 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.69e-01 bond pdb=" CG PRO C 143 " pdb=" CD PRO C 143 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.60e-01 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 272 106.86 - 113.64: 6042 113.64 - 120.42: 3810 120.42 - 127.20: 4309 127.20 - 133.99: 121 Bond angle restraints: 14554 Sorted by residual: angle pdb=" CA PRO F 184 " pdb=" N PRO F 184 " pdb=" CD PRO F 184 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA PRO D 184 " pdb=" N PRO D 184 " pdb=" CD PRO D 184 " ideal model delta sigma weight residual 112.00 108.79 3.21 1.40e+00 5.10e-01 5.26e+00 angle pdb=" CA LYS A 157 " pdb=" CB LYS A 157 " pdb=" CG LYS A 157 " ideal model delta sigma weight residual 114.10 118.63 -4.53 2.00e+00 2.50e-01 5.12e+00 angle pdb=" CB ARG A 202 " pdb=" CG ARG A 202 " pdb=" CD ARG A 202 " ideal model delta sigma weight residual 111.30 116.36 -5.06 2.30e+00 1.89e-01 4.83e+00 angle pdb=" C GLU E 189 " pdb=" N LYS E 190 " pdb=" CA LYS E 190 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 ... (remaining 14549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5735 17.87 - 35.74: 485 35.74 - 53.61: 112 53.61 - 71.48: 9 71.48 - 89.35: 13 Dihedral angle restraints: 6354 sinusoidal: 2380 harmonic: 3974 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 138.65 -45.65 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual 93.00 138.26 -45.26 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA SER E 61 " pdb=" C SER E 61 " pdb=" N ARG E 62 " pdb=" CA ARG E 62 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 6351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1088 0.031 - 0.062: 423 0.062 - 0.093: 106 0.093 - 0.125: 71 0.125 - 0.156: 6 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1691 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 183 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO F 184 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 183 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO D 184 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 184 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 184 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 80 " 0.055 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO E 81 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " 0.045 5.00e-02 4.00e+02 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 152 2.65 - 3.21: 9666 3.21 - 3.77: 15296 3.77 - 4.34: 20644 4.34 - 4.90: 34157 Nonbonded interactions: 79915 Sorted by model distance: nonbonded pdb=" OD2 ASP A 70 " pdb="ZN ZN A 302 " model vdw 2.084 2.230 nonbonded pdb=" OD2 ASP B 70 " pdb="ZN ZN B 302 " model vdw 2.086 2.230 nonbonded pdb=" OD2 ASP A 159 " pdb="ZN ZN A 303 " model vdw 2.140 2.230 nonbonded pdb=" OD2 ASP B 159 " pdb="ZN ZN B 303 " model vdw 2.143 2.230 nonbonded pdb=" O PHE A 49 " pdb=" OG1 THR A 52 " model vdw 2.162 2.440 ... (remaining 79910 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 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 28 5.16 5 C 6676 2.51 5 N 1760 2.21 5 O 2000 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 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: 2.540 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: 0.000 Extract box with map and model: 8.350 Check model and map are aligned: 0.160 Process input model: 30.080 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.003 0.084 10692 Z= 0.189 Angle : 0.514 6.581 14554 Z= 0.260 Chirality : 0.040 0.156 1694 Planarity : 0.005 0.108 1832 Dihedral : 14.392 89.354 3770 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.50 (0.24), residues: 1342 helix: 0.33 (0.27), residues: 366 sheet: -0.11 (0.29), residues: 370 loop : -0.78 (0.27), residues: 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2473 time to fit residues: 61.7805 Evaluate side-chains 155 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN E 160 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10692 Z= 0.262 Angle : 0.599 9.512 14554 Z= 0.312 Chirality : 0.044 0.151 1694 Planarity : 0.005 0.074 1832 Dihedral : 4.344 25.397 1466 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.38 % Favored : 92.25 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.61 (0.24), residues: 1342 helix: 0.46 (0.26), residues: 390 sheet: -0.31 (0.28), residues: 400 loop : -1.00 (0.28), residues: 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.163 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 177 average time/residue: 0.2323 time to fit residues: 58.3143 Evaluate side-chains 157 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0958 time to fit residues: 3.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 10692 Z= 0.237 Angle : 0.562 12.210 14554 Z= 0.292 Chirality : 0.042 0.140 1694 Planarity : 0.004 0.065 1832 Dihedral : 4.293 25.838 1466 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.86 % Favored : 92.85 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.59 (0.24), residues: 1342 helix: 0.61 (0.26), residues: 390 sheet: -0.37 (0.27), residues: 398 loop : -1.03 (0.28), residues: 554 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.189 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 164 average time/residue: 0.2443 time to fit residues: 56.3790 Evaluate side-chains 159 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0963 time to fit residues: 2.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 0.0370 chunk 129 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 0.0470 overall best weight: 0.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10692 Z= 0.132 Angle : 0.528 11.920 14554 Z= 0.268 Chirality : 0.041 0.203 1694 Planarity : 0.004 0.058 1832 Dihedral : 3.992 25.902 1466 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.92 % Favored : 94.78 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.51 (0.24), residues: 1342 helix: 0.62 (0.26), residues: 392 sheet: -0.06 (0.28), residues: 382 loop : -1.15 (0.28), residues: 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.083 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 182 average time/residue: 0.2250 time to fit residues: 58.2110 Evaluate side-chains 159 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0899 time to fit residues: 2.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0060 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 248 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10692 Z= 0.143 Angle : 0.545 12.620 14554 Z= 0.274 Chirality : 0.040 0.139 1694 Planarity : 0.004 0.054 1832 Dihedral : 3.927 25.894 1466 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.14 % Favored : 94.56 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.40 (0.24), residues: 1342 helix: 0.92 (0.26), residues: 380 sheet: -0.05 (0.28), residues: 382 loop : -1.18 (0.27), residues: 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 0.2364 time to fit residues: 55.4724 Evaluate side-chains 157 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1000 time to fit residues: 2.7517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 10692 Z= 0.336 Angle : 0.614 10.677 14554 Z= 0.317 Chirality : 0.043 0.143 1694 Planarity : 0.004 0.054 1832 Dihedral : 4.302 25.287 1466 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.75 % Favored : 91.95 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.63 (0.24), residues: 1342 helix: 0.86 (0.26), residues: 380 sheet: -0.44 (0.27), residues: 404 loop : -1.23 (0.27), residues: 558 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.265 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.2409 time to fit residues: 57.5160 Evaluate side-chains 161 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0882 time to fit residues: 2.5980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN C 160 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10692 Z= 0.258 Angle : 0.594 12.994 14554 Z= 0.302 Chirality : 0.042 0.144 1694 Planarity : 0.004 0.052 1832 Dihedral : 4.277 24.520 1466 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.78 % Favored : 92.85 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.61 (0.24), residues: 1342 helix: 0.92 (0.26), residues: 376 sheet: -0.45 (0.27), residues: 402 loop : -1.22 (0.27), residues: 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.120 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 178 average time/residue: 0.2555 time to fit residues: 64.4242 Evaluate side-chains 168 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1087 time to fit residues: 2.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN A 248 GLN C 160 ASN D 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10692 Z= 0.214 Angle : 0.583 12.247 14554 Z= 0.295 Chirality : 0.042 0.171 1694 Planarity : 0.004 0.051 1832 Dihedral : 4.214 24.482 1466 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.30 % Favored : 92.40 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.59 (0.24), residues: 1342 helix: 0.93 (0.26), residues: 376 sheet: -0.41 (0.27), residues: 402 loop : -1.21 (0.27), residues: 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.286 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 169 average time/residue: 0.2175 time to fit residues: 52.7950 Evaluate side-chains 163 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1005 time to fit residues: 2.2378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 10692 Z= 0.268 Angle : 0.608 12.026 14554 Z= 0.307 Chirality : 0.043 0.145 1694 Planarity : 0.004 0.051 1832 Dihedral : 4.339 24.386 1466 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.38 % Favored : 92.32 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.66 (0.24), residues: 1342 helix: 0.90 (0.27), residues: 382 sheet: -0.47 (0.27), residues: 402 loop : -1.30 (0.27), residues: 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 1.191 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 163 average time/residue: 0.2218 time to fit residues: 51.6504 Evaluate side-chains 160 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0952 time to fit residues: 1.8152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 133 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10692 Z= 0.218 Angle : 0.586 12.113 14554 Z= 0.295 Chirality : 0.042 0.148 1694 Planarity : 0.004 0.050 1832 Dihedral : 4.236 24.793 1466 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.00 % Favored : 92.70 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.61 (0.24), residues: 1342 helix: 0.96 (0.27), residues: 382 sheet: -0.45 (0.27), residues: 402 loop : -1.27 (0.27), residues: 558 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.276 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2420 time to fit residues: 55.3918 Evaluate side-chains 159 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.4980 chunk 93 optimal weight: 0.0040 chunk 6 optimal weight: 5.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN C 160 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.207436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148332 restraints weight = 12535.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146066 restraints weight = 18312.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142518 restraints weight = 16687.612| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 10692 Z= 0.158 Angle : 0.575 11.864 14554 Z= 0.286 Chirality : 0.041 0.146 1694 Planarity : 0.004 0.050 1832 Dihedral : 4.065 24.657 1466 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.29 % Favored : 94.41 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.51 (0.24), residues: 1342 helix: 1.01 (0.27), residues: 382 sheet: -0.25 (0.27), residues: 406 loop : -1.31 (0.27), residues: 554 =============================================================================== Job complete usr+sys time: 2137.53 seconds wall clock time: 40 minutes 2.07 seconds (2402.07 seconds total)