Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 07:29:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/10_2023/8f6i_28884.pdb" } resolution = 4.03 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= 0.000 sd= 0.013 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 6 6.06 5 S 28 5.16 5 C 6620 2.51 5 N 1734 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10367 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2132 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 6, 'TRANS': 269} Chain breaks: 1 Chain: "A" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2112 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 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: "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: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1580 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.88, per 1000 atoms: 0.57 Number of scatterers: 10367 At special positions: 0 Unit cell: (67.977, 157.534, 149.981, 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 6 29.99 S 28 16.00 O 1979 8.00 N 1734 7.00 C 6620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 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: 4.18 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 250 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 31.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 8 through 37 removed outlier: 3.596A pdb=" N LYS B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.821A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 103 removed outlier: 3.721A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 115 through 141 removed outlier: 4.030A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 175 removed outlier: 4.194A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.795A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.673A pdb=" N SER B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.677A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.531A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 105 removed outlier: 3.769A pdb=" N GLU A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 removed outlier: 4.130A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 176 removed outlier: 4.229A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.632A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 258 through 277 Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.939A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.799A pdb=" N SER F 34 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 35' Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.702A pdb=" N LEU C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 128' Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.741A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 185 through 189' Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.710A pdb=" N LYS D 68 " --> pdb=" O ASP D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 171 through 175 Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.349A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE B 283 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 247 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS B 285 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 249 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP B 287 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU B 251 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 5.920A pdb=" N LEU A 233 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU A 252 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS A 250 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 283 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 285 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.701A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AA5, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.835A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 116 through 120 removed outlier: 3.854A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 178 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AA8, first strand: chain 'F' and resid 8 through 10 Processing sheet with id=AA9, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.866A pdb=" N THR F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 127 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.866A pdb=" N THR F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 127 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS F 99 " --> pdb=" O TRP F 121 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP F 121 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG F 101 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.550A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.550A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 167 through 171 removed outlier: 4.118A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN F 216 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 170 " --> pdb=" O ASN F 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (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 11 through 14 removed outlier: 3.571A pdb=" N THR C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 38 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.021A pdb=" N ILE C 92 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR C 99 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 94 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.795A pdb=" N VAL C 135 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.621A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 24 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 84 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.700A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS D 99 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP D 121 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 101 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.700A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 137 through 141 removed outlier: 4.080A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.677A pdb=" N CYS D 213 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS D 226 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 215 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 224 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS D 217 " --> pdb=" O THR D 222 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1359 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: 2.83 Time building geometry restraints manager: 4.52 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: 3303 1.34 - 1.46: 2572 1.46 - 1.58: 4672 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 10585 Sorted by residual: bond pdb=" CB GLU F 92 " pdb=" CG GLU F 92 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.06e-01 bond pdb=" CA ASP C 2 " pdb=" CB ASP C 2 " ideal model delta sigma weight residual 1.527 1.550 -0.023 2.48e-02 1.63e+03 8.64e-01 bond pdb=" CG PRO C 9 " pdb=" CD PRO C 9 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.32e-01 bond pdb=" C GLN C 39 " pdb=" N LYS C 40 " ideal model delta sigma weight residual 1.339 1.299 0.040 5.57e-02 3.22e+02 5.24e-01 bond pdb=" CG GLU F 92 " pdb=" CD GLU F 92 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.21e-01 ... (remaining 10580 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 272 107.07 - 113.80: 6053 113.80 - 120.53: 3911 120.53 - 127.27: 4058 127.27 - 134.00: 111 Bond angle restraints: 14405 Sorted by residual: angle pdb=" C LEU A 34 " pdb=" N TYR A 35 " pdb=" CA TYR A 35 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" N ARG D 111 " pdb=" CA ARG D 111 " pdb=" C ARG D 111 " ideal model delta sigma weight residual 110.80 115.45 -4.65 2.13e+00 2.20e-01 4.77e+00 angle pdb=" N ASP F 93 " pdb=" CA ASP F 93 " pdb=" C ASP F 93 " ideal model delta sigma weight residual 114.09 110.71 3.38 1.55e+00 4.16e-01 4.77e+00 angle pdb=" N ASP B 181 " pdb=" CA ASP B 181 " pdb=" CB ASP B 181 " ideal model delta sigma weight residual 113.65 110.65 3.00 1.47e+00 4.63e-01 4.16e+00 angle pdb=" N HIS D 112 " pdb=" CA HIS D 112 " pdb=" C HIS D 112 " ideal model delta sigma weight residual 107.75 111.53 -3.78 1.86e+00 2.89e-01 4.12e+00 ... (remaining 14400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5670 17.75 - 35.51: 506 35.51 - 53.26: 85 53.26 - 71.01: 12 71.01 - 88.77: 9 Dihedral angle restraints: 6282 sinusoidal: 2355 harmonic: 3927 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 213 " pdb=" CB CYS D 213 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+01 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 93.00 169.27 -76.27 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 161.97 -68.97 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 977 0.026 - 0.052: 443 0.052 - 0.077: 127 0.077 - 0.103: 96 0.103 - 0.129: 35 Chirality restraints: 1678 Sorted by residual: 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 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL C 59 " pdb=" N VAL C 59 " pdb=" C VAL C 59 " pdb=" CB VAL C 59 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1675 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 95 " -0.009 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP E 95 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP E 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 95 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 95 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 95 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 95 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 95 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 95 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 95 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO F 166 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 59 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO E 60 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 124 2.64 - 3.20: 9490 3.20 - 3.77: 15411 3.77 - 4.33: 20115 4.33 - 4.90: 32598 Nonbonded interactions: 77738 Sorted by model distance: nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 302 " model vdw 2.070 2.230 nonbonded pdb=" OD1 ASP A 287 " pdb="ZN ZN A 301 " model vdw 2.071 2.230 nonbonded pdb=" OD1 ASP B 47 " pdb="ZN ZN B 303 " model vdw 2.092 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 301 " model vdw 2.093 2.230 nonbonded pdb=" OD2 ASP B 51 " pdb="ZN ZN B 303 " model vdw 2.100 2.230 ... (remaining 77733 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' and (resid 9 through 63 or resid 78 through 292 or resid 301 through \ 303)) selection = (chain 'B' and (resid 9 through 63 or resid 78 through 292 or resid 301 through \ 303)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and resid 5 through 230) } 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: 1.870 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: 7.880 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.070 Find NCS groups from input model: 0.620 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.002 0.040 10585 Z= 0.141 Angle : 0.504 6.040 14405 Z= 0.254 Chirality : 0.039 0.129 1678 Planarity : 0.003 0.042 1808 Dihedral : 13.671 86.096 3729 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.18 (0.24), residues: 1323 helix: 1.17 (0.27), residues: 377 sheet: 0.45 (0.27), residues: 379 loop : -0.78 (0.27), residues: 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.226 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2112 time to fit residues: 46.7127 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10585 Z= 0.324 Angle : 0.606 9.162 14405 Z= 0.322 Chirality : 0.043 0.161 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.156 24.480 1446 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.23 (0.23), residues: 1323 helix: 1.59 (0.27), residues: 387 sheet: 0.28 (0.27), residues: 368 loop : -0.93 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.193 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2117 time to fit residues: 50.7365 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10585 Z= 0.318 Angle : 0.600 8.328 14405 Z= 0.313 Chirality : 0.042 0.185 1678 Planarity : 0.004 0.045 1808 Dihedral : 4.293 24.812 1446 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.06 (0.23), residues: 1323 helix: 1.55 (0.26), residues: 389 sheet: 0.06 (0.27), residues: 362 loop : -1.01 (0.26), residues: 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2270 time to fit residues: 54.6313 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10585 Z= 0.219 Angle : 0.554 7.545 14405 Z= 0.288 Chirality : 0.041 0.145 1678 Planarity : 0.004 0.070 1808 Dihedral : 4.167 25.945 1446 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.06 (0.23), residues: 1323 helix: 1.55 (0.26), residues: 388 sheet: 0.10 (0.27), residues: 371 loop : -1.06 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2219 time to fit residues: 52.3581 Evaluate side-chains 122 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 10585 Z= 0.293 Angle : 0.600 8.172 14405 Z= 0.309 Chirality : 0.043 0.170 1678 Planarity : 0.004 0.065 1808 Dihedral : 4.345 21.732 1446 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.07 (0.23), residues: 1323 helix: 1.66 (0.26), residues: 386 sheet: 0.06 (0.27), residues: 370 loop : -1.07 (0.26), residues: 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2179 time to fit residues: 51.2116 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 42 GLN F 188 GLN F 216 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10585 Z= 0.177 Angle : 0.561 6.553 14405 Z= 0.284 Chirality : 0.041 0.151 1678 Planarity : 0.004 0.045 1808 Dihedral : 4.161 22.645 1446 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.14 (0.23), residues: 1323 helix: 1.68 (0.27), residues: 386 sheet: 0.02 (0.26), residues: 378 loop : -0.94 (0.26), residues: 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2217 time to fit residues: 52.7732 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.0010 chunk 71 optimal weight: 0.1980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 58 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN D 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10585 Z= 0.136 Angle : 0.553 6.518 14405 Z= 0.278 Chirality : 0.041 0.160 1678 Planarity : 0.004 0.043 1808 Dihedral : 3.978 22.262 1446 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.09 % Allowed : 1.32 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.29 (0.23), residues: 1323 helix: 1.73 (0.27), residues: 384 sheet: 0.12 (0.26), residues: 394 loop : -0.83 (0.27), residues: 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2199 time to fit residues: 54.2370 Evaluate side-chains 134 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10585 Z= 0.304 Angle : 0.608 10.237 14405 Z= 0.313 Chirality : 0.043 0.200 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.244 22.848 1446 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.25 (0.23), residues: 1323 helix: 1.75 (0.27), residues: 383 sheet: 0.20 (0.26), residues: 381 loop : -0.96 (0.26), residues: 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2123 time to fit residues: 48.1068 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 216 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10585 Z= 0.188 Angle : 0.584 9.654 14405 Z= 0.294 Chirality : 0.042 0.182 1678 Planarity : 0.004 0.043 1808 Dihedral : 4.198 21.936 1446 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.20 (0.23), residues: 1323 helix: 1.65 (0.26), residues: 384 sheet: 0.20 (0.26), residues: 376 loop : -0.96 (0.26), residues: 563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.2195 time to fit residues: 49.9908 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10585 Z= 0.307 Angle : 0.617 8.927 14405 Z= 0.320 Chirality : 0.043 0.182 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.363 25.148 1446 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.16 (0.23), residues: 1323 helix: 1.72 (0.26), residues: 384 sheet: 0.09 (0.26), residues: 375 loop : -1.00 (0.26), residues: 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.2168 time to fit residues: 47.8010 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 216 ASN D 85 GLN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.125177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096258 restraints weight = 24896.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095480 restraints weight = 34058.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096305 restraints weight = 24163.150| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 10585 Z= 0.318 Angle : 0.627 8.760 14405 Z= 0.324 Chirality : 0.043 0.177 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.499 25.776 1446 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.05 (0.23), residues: 1323 helix: 1.63 (0.26), residues: 385 sheet: -0.03 (0.26), residues: 377 loop : -1.03 (0.26), residues: 561 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.69 seconds wall clock time: 38 minutes 48.31 seconds (2328.31 seconds total)