Starting phenix.real_space_refine on Wed Feb 14 23:11:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2024/8f6j_28885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2024/8f6j_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_2024/8f6j_28885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2024/8f6j_28885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2024/8f6j_28885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6j_28885/02_2024/8f6j_28885.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 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. 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-5238/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: 6.51, per 1000 atoms: 0.62 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: 4.58 Conformation dependent library (CDL) restraints added in 2.0 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: 1.19 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: 2.96 Time building geometry restraints manager: 4.86 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 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.890 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.990 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 6.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS A 155 PHE 0.022 0.001 PHE A 49 TYR 0.008 0.001 TYR E 50 ARG 0.004 0.000 ARG A 202 *********************** 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 : 1.131 Fit side-chains REVERT: A 41 MET cc_start: 0.7181 (pmm) cc_final: 0.6967 (pmm) REVERT: A 101 PHE cc_start: 0.8444 (t80) cc_final: 0.8113 (t80) REVERT: A 202 ARG cc_start: 0.8272 (pmt170) cc_final: 0.8005 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2270 time to fit residues: 56.4920 Evaluate side-chains 155 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7885 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10692 Z= 0.262 Angle : 0.593 9.630 14554 Z= 0.311 Chirality : 0.043 0.186 1694 Planarity : 0.005 0.075 1832 Dihedral : 4.266 25.387 1466 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.38 % Favored : 92.25 % Rotamer: Outliers : 1.22 % Allowed : 12.41 % Favored : 86.36 % 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: -0.60 (0.24), residues: 1342 helix: 0.51 (0.26), residues: 390 sheet: -0.30 (0.28), residues: 412 loop : -1.03 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 33 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.001 PHE B 49 TYR 0.019 0.002 TYR D 162 ARG 0.004 0.000 ARG B 202 *********************** 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 177 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.135 Fit side-chains REVERT: B 101 PHE cc_start: 0.8326 (t80) cc_final: 0.8104 (t80) REVERT: B 202 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7980 (mtm180) REVERT: F 162 TYR cc_start: 0.7954 (p90) cc_final: 0.7563 (p90) REVERT: A 101 PHE cc_start: 0.8316 (t80) cc_final: 0.7977 (t80) REVERT: D 162 TYR cc_start: 0.8008 (p90) cc_final: 0.7562 (p90) REVERT: D 226 LYS cc_start: 0.8031 (tppp) cc_final: 0.7641 (tptp) outliers start: 14 outliers final: 12 residues processed: 173 average time/residue: 0.2289 time to fit residues: 55.7782 Evaluate side-chains 156 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN 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: 0.9980 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** 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: 0.7896 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10692 Z= 0.254 Angle : 0.568 9.609 14554 Z= 0.297 Chirality : 0.042 0.144 1694 Planarity : 0.004 0.064 1832 Dihedral : 4.319 25.854 1466 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.08 % Favored : 92.55 % Rotamer: Outliers : 1.84 % Allowed : 15.03 % Favored : 83.13 % 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: -0.60 (0.24), residues: 1342 helix: 0.61 (0.26), residues: 390 sheet: -0.37 (0.28), residues: 398 loop : -1.04 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 50 HIS 0.003 0.001 HIS B 155 PHE 0.018 0.002 PHE A 97 TYR 0.020 0.001 TYR C 142 ARG 0.002 0.000 ARG A 202 *********************** 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 177 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.123 Fit side-chains REVERT: B 99 LEU cc_start: 0.8497 (mt) cc_final: 0.8120 (mt) REVERT: F 226 LYS cc_start: 0.8011 (tppp) cc_final: 0.7609 (tptp) REVERT: A 101 PHE cc_start: 0.8373 (t80) cc_final: 0.8161 (t80) REVERT: A 205 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7110 (mm-40) REVERT: D 226 LYS cc_start: 0.8025 (tppp) cc_final: 0.7614 (tptp) outliers start: 21 outliers final: 16 residues processed: 171 average time/residue: 0.2323 time to fit residues: 55.5863 Evaluate side-chains 169 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 223 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 107 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10692 Z= 0.176 Angle : 0.535 9.591 14554 Z= 0.277 Chirality : 0.042 0.236 1694 Planarity : 0.004 0.059 1832 Dihedral : 4.180 25.850 1466 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 2.62 % Allowed : 16.70 % Favored : 80.68 % 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: 0.61 (0.26), residues: 390 sheet: -0.34 (0.27), residues: 406 loop : -1.11 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.023 0.001 PHE A 49 TYR 0.017 0.001 TYR C 142 ARG 0.006 0.000 ARG B 202 *********************** 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 196 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.513 Fit side-chains REVERT: F 162 TYR cc_start: 0.7963 (p90) cc_final: 0.7540 (p90) REVERT: F 226 LYS cc_start: 0.7941 (tppp) cc_final: 0.7435 (tptp) REVERT: A 101 PHE cc_start: 0.8287 (t80) cc_final: 0.7966 (t80) REVERT: C 91 GLN cc_start: 0.8611 (pp30) cc_final: 0.8257 (pp30) REVERT: D 162 TYR cc_start: 0.8007 (p90) cc_final: 0.7547 (p90) REVERT: D 226 LYS cc_start: 0.7922 (tppp) cc_final: 0.7387 (tptp) outliers start: 30 outliers final: 21 residues processed: 185 average time/residue: 0.2409 time to fit residues: 63.0212 Evaluate side-chains 170 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 D 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10692 Z= 0.178 Angle : 0.558 12.847 14554 Z= 0.282 Chirality : 0.041 0.197 1694 Planarity : 0.004 0.056 1832 Dihedral : 4.129 25.963 1466 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.48 % Favored : 93.22 % Rotamer: Outliers : 2.53 % Allowed : 17.92 % Favored : 79.55 % 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: 0.65 (0.26), residues: 392 sheet: -0.17 (0.28), residues: 382 loop : -1.25 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 33 HIS 0.003 0.001 HIS B 155 PHE 0.019 0.001 PHE A 97 TYR 0.015 0.001 TYR E 142 ARG 0.009 0.000 ARG B 202 *********************** 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 193 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: B 101 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80) REVERT: B 191 TYR cc_start: 0.7584 (t80) cc_final: 0.7234 (t80) REVERT: B 205 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7391 (tp40) REVERT: E 91 GLN cc_start: 0.8702 (pp30) cc_final: 0.8380 (pp30) REVERT: E 169 ASP cc_start: 0.8531 (m-30) cc_final: 0.7936 (m-30) REVERT: F 226 LYS cc_start: 0.7931 (tppp) cc_final: 0.7408 (tptp) REVERT: A 33 TRP cc_start: 0.5687 (t60) cc_final: 0.5454 (t60) REVERT: C 91 GLN cc_start: 0.8603 (pp30) cc_final: 0.8272 (pp30) REVERT: C 169 ASP cc_start: 0.8520 (m-30) cc_final: 0.7881 (m-30) REVERT: D 226 LYS cc_start: 0.7930 (tppp) cc_final: 0.7385 (tptp) outliers start: 29 outliers final: 21 residues processed: 184 average time/residue: 0.2440 time to fit residues: 62.7578 Evaluate side-chains 178 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 ASN 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: 0.6980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 0.0980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10692 Z= 0.152 Angle : 0.544 10.304 14554 Z= 0.275 Chirality : 0.041 0.197 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.032 25.448 1466 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.44 % Favored : 94.26 % Rotamer: Outliers : 2.88 % Allowed : 18.62 % Favored : 78.50 % 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: 0.86 (0.26), residues: 380 sheet: -0.10 (0.28), residues: 382 loop : -1.27 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.024 0.001 PHE A 49 TYR 0.013 0.001 TYR E 142 ARG 0.006 0.000 ARG B 202 *********************** 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 200 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: B 101 PHE cc_start: 0.8320 (t80) cc_final: 0.8073 (t80) REVERT: B 191 TYR cc_start: 0.7582 (t80) cc_final: 0.7251 (t80) REVERT: B 202 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7804 (mtm180) REVERT: B 205 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7381 (mm110) REVERT: E 91 GLN cc_start: 0.8609 (pp30) cc_final: 0.8363 (pp30) REVERT: E 169 ASP cc_start: 0.8527 (m-30) cc_final: 0.7953 (m-30) REVERT: F 162 TYR cc_start: 0.7971 (p90) cc_final: 0.7561 (p90) REVERT: F 226 LYS cc_start: 0.7915 (tppp) cc_final: 0.7397 (tptp) REVERT: A 23 LEU cc_start: 0.8528 (tp) cc_final: 0.8306 (tt) REVERT: A 33 TRP cc_start: 0.5850 (t60) cc_final: 0.5333 (t60) REVERT: A 41 MET cc_start: 0.7552 (pmm) cc_final: 0.7073 (pmm) REVERT: A 101 PHE cc_start: 0.8444 (t80) cc_final: 0.8048 (t80) REVERT: A 102 TYR cc_start: 0.7542 (t80) cc_final: 0.7229 (t80) REVERT: C 91 GLN cc_start: 0.8502 (pp30) cc_final: 0.8257 (pp30) REVERT: C 169 ASP cc_start: 0.8528 (m-30) cc_final: 0.7862 (m-30) REVERT: D 162 TYR cc_start: 0.8012 (p90) cc_final: 0.7607 (p90) REVERT: D 226 LYS cc_start: 0.7930 (tppp) cc_final: 0.7400 (tptp) outliers start: 33 outliers final: 23 residues processed: 191 average time/residue: 0.2145 time to fit residues: 58.1734 Evaluate side-chains 190 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 129 optimal weight: 0.0870 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 overall best weight: 1.8340 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10692 Z= 0.460 Angle : 0.675 12.868 14554 Z= 0.347 Chirality : 0.045 0.171 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.561 25.556 1466 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.20 % Favored : 91.43 % Rotamer: Outliers : 3.23 % Allowed : 19.23 % Favored : 77.53 % 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: -0.79 (0.23), residues: 1342 helix: 0.67 (0.26), residues: 378 sheet: -0.53 (0.27), residues: 402 loop : -1.25 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 33 HIS 0.006 0.001 HIS B 234 PHE 0.017 0.002 PHE A 101 TYR 0.012 0.002 TYR E 88 ARG 0.005 0.001 ARG A 106 *********************** 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 199 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 205 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7231 (mm-40) REVERT: E 169 ASP cc_start: 0.8533 (m-30) cc_final: 0.7923 (m-30) REVERT: A 40 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7305 (t) REVERT: A 41 MET cc_start: 0.7551 (pmm) cc_final: 0.7300 (pmm) REVERT: A 101 PHE cc_start: 0.8550 (t80) cc_final: 0.8181 (t80) REVERT: A 102 TYR cc_start: 0.7669 (t80) cc_final: 0.7255 (t80) REVERT: A 141 LEU cc_start: 0.1785 (OUTLIER) cc_final: 0.1401 (mp) REVERT: C 169 ASP cc_start: 0.8532 (m-30) cc_final: 0.7854 (m-30) REVERT: C 174 THR cc_start: 0.9037 (t) cc_final: 0.8676 (t) REVERT: D 226 LYS cc_start: 0.7940 (tppp) cc_final: 0.7274 (tptp) outliers start: 37 outliers final: 30 residues processed: 190 average time/residue: 0.2137 time to fit residues: 57.5450 Evaluate side-chains 190 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10692 Z= 0.203 Angle : 0.580 12.009 14554 Z= 0.293 Chirality : 0.042 0.176 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.300 24.532 1466 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % Rotamer: Outliers : 2.45 % Allowed : 21.77 % Favored : 75.79 % 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: 0.78 (0.27), residues: 374 sheet: -0.42 (0.27), residues: 402 loop : -1.20 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.019 0.001 PHE A 101 TYR 0.012 0.001 TYR C 142 ARG 0.006 0.000 ARG B 202 *********************** 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 196 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: B 202 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7606 (mtm180) REVERT: B 205 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7432 (tp40) REVERT: E 91 GLN cc_start: 0.8707 (pp30) cc_final: 0.8326 (pp30) REVERT: E 169 ASP cc_start: 0.8503 (m-30) cc_final: 0.7907 (m-30) REVERT: F 226 LYS cc_start: 0.7762 (tppp) cc_final: 0.7246 (tmtt) REVERT: A 33 TRP cc_start: 0.5781 (t60) cc_final: 0.5546 (t60) REVERT: A 41 MET cc_start: 0.7397 (pmm) cc_final: 0.6981 (pmm) REVERT: A 101 PHE cc_start: 0.8419 (t80) cc_final: 0.7973 (t80) REVERT: A 102 TYR cc_start: 0.7643 (t80) cc_final: 0.7321 (t80) REVERT: A 141 LEU cc_start: 0.1958 (OUTLIER) cc_final: 0.1592 (mp) REVERT: C 91 GLN cc_start: 0.8615 (pp30) cc_final: 0.8215 (pp30) REVERT: C 169 ASP cc_start: 0.8512 (m-30) cc_final: 0.7836 (m-30) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.2207 time to fit residues: 59.5237 Evaluate side-chains 187 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10692 Z= 0.238 Angle : 0.595 11.647 14554 Z= 0.299 Chirality : 0.042 0.180 1694 Planarity : 0.004 0.052 1832 Dihedral : 4.283 24.638 1466 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.15 % Favored : 92.47 % Rotamer: Outliers : 2.45 % Allowed : 22.38 % Favored : 75.17 % 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: -0.62 (0.24), residues: 1342 helix: 0.82 (0.26), residues: 374 sheet: -0.45 (0.27), residues: 412 loop : -1.14 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.018 0.002 PHE A 101 TYR 0.011 0.001 TYR C 142 ARG 0.004 0.000 ARG A 106 *********************** 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 194 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: B 205 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (mm110) REVERT: E 91 GLN cc_start: 0.8711 (pp30) cc_final: 0.8335 (pp30) REVERT: E 160 ASN cc_start: 0.8587 (m-40) cc_final: 0.7969 (t0) REVERT: E 169 ASP cc_start: 0.8539 (m-30) cc_final: 0.7923 (m-30) REVERT: F 226 LYS cc_start: 0.7751 (tppp) cc_final: 0.7218 (tmtt) REVERT: A 23 LEU cc_start: 0.8563 (tp) cc_final: 0.8324 (tt) REVERT: A 41 MET cc_start: 0.7310 (pmm) cc_final: 0.6939 (pmm) REVERT: A 101 PHE cc_start: 0.8433 (t80) cc_final: 0.7974 (t80) REVERT: A 102 TYR cc_start: 0.7747 (t80) cc_final: 0.7446 (t80) REVERT: A 141 LEU cc_start: 0.2010 (OUTLIER) cc_final: 0.1651 (mp) REVERT: C 91 GLN cc_start: 0.8616 (pp30) cc_final: 0.8219 (pp30) REVERT: C 169 ASP cc_start: 0.8526 (m-30) cc_final: 0.7838 (m-30) REVERT: D 226 LYS cc_start: 0.7781 (tppp) cc_final: 0.7228 (tmtt) outliers start: 28 outliers final: 25 residues processed: 188 average time/residue: 0.2188 time to fit residues: 58.5214 Evaluate side-chains 191 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 0.0870 chunk 122 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 113 optimal weight: 0.0030 overall best weight: 0.5168 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10692 Z= 0.189 Angle : 0.586 11.639 14554 Z= 0.292 Chirality : 0.042 0.188 1694 Planarity : 0.004 0.051 1832 Dihedral : 4.191 24.710 1466 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 2.45 % Allowed : 22.12 % Favored : 75.44 % 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: -0.58 (0.24), residues: 1342 helix: 0.88 (0.26), residues: 376 sheet: -0.38 (0.27), residues: 402 loop : -1.18 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.018 0.001 PHE A 101 TYR 0.011 0.001 TYR C 142 ARG 0.008 0.000 ARG B 202 ********************** 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 193 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: E 91 GLN cc_start: 0.8671 (pp30) cc_final: 0.8363 (pp30) REVERT: E 160 ASN cc_start: 0.8600 (m-40) cc_final: 0.7983 (t0) REVERT: E 169 ASP cc_start: 0.8511 (m-30) cc_final: 0.7887 (m-30) REVERT: F 226 LYS cc_start: 0.7770 (tppp) cc_final: 0.7220 (tmtt) REVERT: A 41 MET cc_start: 0.7227 (pmm) cc_final: 0.6785 (pmm) REVERT: A 101 PHE cc_start: 0.8449 (t80) cc_final: 0.7996 (t80) REVERT: A 102 TYR cc_start: 0.7746 (t80) cc_final: 0.7473 (t80) REVERT: A 141 LEU cc_start: 0.2027 (OUTLIER) cc_final: 0.1672 (mp) REVERT: C 91 GLN cc_start: 0.8563 (pp30) cc_final: 0.8249 (pp30) REVERT: C 163 GLU cc_start: 0.8355 (pm20) cc_final: 0.8116 (pm20) REVERT: C 169 ASP cc_start: 0.8504 (m-30) cc_final: 0.7835 (m-30) outliers start: 28 outliers final: 25 residues processed: 186 average time/residue: 0.2187 time to fit residues: 58.0391 Evaluate side-chains 190 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 C 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.206147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147301 restraints weight = 12546.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143561 restraints weight = 19345.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142304 restraints weight = 17503.282| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2637 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= 0.190 Angle : 0.579 11.539 14554 Z= 0.289 Chirality : 0.041 0.197 1694 Planarity : 0.004 0.051 1832 Dihedral : 4.138 24.945 1466 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.71 % Favored : 92.92 % Rotamer: Outliers : 2.27 % Allowed : 22.20 % Favored : 75.52 % 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: -0.52 (0.24), residues: 1342 helix: 0.94 (0.27), residues: 376 sheet: -0.34 (0.27), residues: 402 loop : -1.16 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 33 HIS 0.003 0.001 HIS B 155 PHE 0.018 0.002 PHE A 101 TYR 0.011 0.001 TYR E 142 ARG 0.004 0.000 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.62 seconds wall clock time: 42 minutes 28.39 seconds (2548.39 seconds total)