Starting phenix.real_space_refine on Fri Mar 15 02:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/03_2024/8f6i_28884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/03_2024/8f6i_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_28884/03_2024/8f6i_28884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/03_2024/8f6i_28884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/03_2024/8f6i_28884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6i_28884/03_2024/8f6i_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-dev-5265/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: 5.71, per 1000 atoms: 0.55 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: 3.94 Conformation dependent library (CDL) restraints added in 1.6 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: 0.93 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: 2.81 Time building geometry restraints manager: 4.24 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: 1.460 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: 7.920 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 30.060 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 PHE 0.018 0.001 PHE A 91 TYR 0.014 0.001 TYR F 193 ARG 0.005 0.000 ARG D 111 *********************** 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 : 1.317 Fit side-chains revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8386 (pp30) cc_final: 0.7898 (pp30) REVERT: E 145 GLU cc_start: 0.8161 (mp0) cc_final: 0.7944 (mp0) REVERT: F 161 ASP cc_start: 0.7369 (m-30) cc_final: 0.7169 (m-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2034 time to fit residues: 44.9966 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.6184 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10585 Z= 0.320 Angle : 0.597 8.490 14405 Z= 0.319 Chirality : 0.043 0.164 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.071 24.030 1446 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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: 0.27 (0.23), residues: 1323 helix: 1.58 (0.26), residues: 390 sheet: 0.35 (0.27), residues: 362 loop : -0.90 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 95 HIS 0.008 0.001 HIS A 250 PHE 0.024 0.001 PHE A 249 TYR 0.017 0.001 TYR F 193 ARG 0.004 0.000 ARG B 202 *********************** 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 : 1.311 Fit side-chains REVERT: A 33 TRP cc_start: 0.7118 (t-100) cc_final: 0.6603 (t-100) REVERT: A 88 GLN cc_start: 0.8488 (pp30) cc_final: 0.8073 (pp30) REVERT: A 191 TYR cc_start: 0.8050 (t80) cc_final: 0.7849 (t80) REVERT: A 274 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8945 (ttmm) REVERT: E 91 GLN cc_start: 0.8925 (pp30) cc_final: 0.8478 (pp30) REVERT: E 140 ASN cc_start: 0.8560 (m-40) cc_final: 0.8318 (m-40) REVERT: C 95 TRP cc_start: 0.8192 (t60) cc_final: 0.6961 (t60) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2008 time to fit residues: 47.8455 Evaluate side-chains 122 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 0.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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** ** 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: 0.8008 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10585 Z= 0.250 Angle : 0.565 8.004 14405 Z= 0.293 Chirality : 0.041 0.181 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.132 26.062 1446 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: 0.17 (0.23), residues: 1323 helix: 1.59 (0.26), residues: 389 sheet: 0.16 (0.27), residues: 362 loop : -0.91 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 95 HIS 0.007 0.001 HIS A 250 PHE 0.018 0.001 PHE A 249 TYR 0.012 0.001 TYR E 50 ARG 0.002 0.000 ARG B 229 *********************** 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 171 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8466 (pp30) cc_final: 0.8040 (pp30) REVERT: A 168 LEU cc_start: 0.8989 (pp) cc_final: 0.8775 (mt) REVERT: A 191 TYR cc_start: 0.7999 (t80) cc_final: 0.7768 (t80) REVERT: A 274 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8963 (ttmm) REVERT: E 91 GLN cc_start: 0.8812 (pp30) cc_final: 0.8364 (pp30) REVERT: E 140 ASN cc_start: 0.8600 (m-40) cc_final: 0.8277 (m-40) REVERT: F 160 LYS cc_start: 0.8740 (tppt) cc_final: 0.7995 (tppt) REVERT: F 223 LYS cc_start: 0.8590 (tppt) cc_final: 0.8222 (mmtt) REVERT: C 95 TRP cc_start: 0.8432 (t60) cc_final: 0.7133 (t60) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2103 time to fit residues: 51.0740 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** F 188 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10585 Z= 0.264 Angle : 0.573 7.786 14405 Z= 0.297 Chirality : 0.042 0.148 1678 Planarity : 0.004 0.062 1808 Dihedral : 4.215 24.647 1446 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.74 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 0.13 (0.23), residues: 1323 helix: 1.61 (0.26), residues: 387 sheet: 0.14 (0.27), residues: 361 loop : -0.98 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 95 HIS 0.008 0.001 HIS A 250 PHE 0.015 0.001 PHE D 130 TYR 0.014 0.001 TYR E 50 ARG 0.005 0.000 ARG F 111 *********************** 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 165 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.6822 (t-100) cc_final: 0.6374 (t-100) REVERT: A 88 GLN cc_start: 0.8496 (pp30) cc_final: 0.8009 (pp30) REVERT: A 191 TYR cc_start: 0.8013 (t80) cc_final: 0.7767 (t80) REVERT: A 274 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8950 (ttmm) REVERT: E 91 GLN cc_start: 0.8799 (pp30) cc_final: 0.8192 (pp30) REVERT: E 119 ILE cc_start: 0.7395 (mp) cc_final: 0.7042 (pt) REVERT: E 140 ASN cc_start: 0.8685 (m-40) cc_final: 0.8346 (m-40) REVERT: F 160 LYS cc_start: 0.8770 (tppt) cc_final: 0.7923 (tppt) REVERT: F 161 ASP cc_start: 0.7846 (m-30) cc_final: 0.7646 (m-30) REVERT: C 94 SER cc_start: 0.8944 (m) cc_final: 0.8699 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2164 time to fit residues: 50.2504 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** 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: 0.7988 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10585 Z= 0.206 Angle : 0.552 7.136 14405 Z= 0.282 Chirality : 0.041 0.169 1678 Planarity : 0.004 0.044 1808 Dihedral : 4.138 23.549 1446 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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 (0.23), residues: 1323 helix: 1.73 (0.26), residues: 386 sheet: 0.04 (0.27), residues: 378 loop : -0.94 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 95 HIS 0.007 0.001 HIS B 263 PHE 0.014 0.001 PHE B 97 TYR 0.011 0.001 TYR E 50 ARG 0.008 0.000 ARG C 62 *********************** 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 169 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8354 (t80) cc_final: 0.7867 (t80) REVERT: A 33 TRP cc_start: 0.6835 (t-100) cc_final: 0.6425 (t-100) REVERT: A 88 GLN cc_start: 0.8511 (pp30) cc_final: 0.8045 (pp30) REVERT: A 191 TYR cc_start: 0.8003 (t80) cc_final: 0.7777 (t80) REVERT: A 274 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8949 (ttmm) REVERT: E 119 ILE cc_start: 0.7293 (mp) cc_final: 0.6982 (pt) REVERT: E 140 ASN cc_start: 0.8630 (m-40) cc_final: 0.8312 (m-40) REVERT: F 160 LYS cc_start: 0.8802 (tppt) cc_final: 0.7892 (tppt) REVERT: F 161 ASP cc_start: 0.7858 (m-30) cc_final: 0.7631 (m-30) REVERT: F 187 LEU cc_start: 0.8669 (tp) cc_final: 0.8139 (pp) REVERT: C 94 SER cc_start: 0.8909 (m) cc_final: 0.8702 (p) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2181 time to fit residues: 51.7971 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 188 GLN F 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10585 Z= 0.287 Angle : 0.586 7.090 14405 Z= 0.302 Chirality : 0.042 0.151 1678 Planarity : 0.004 0.045 1808 Dihedral : 4.300 24.312 1446 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % 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: 0.13 (0.23), residues: 1323 helix: 1.67 (0.26), residues: 386 sheet: 0.13 (0.27), residues: 370 loop : -1.04 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 95 HIS 0.006 0.001 HIS B 285 PHE 0.017 0.001 PHE E 141 TYR 0.015 0.001 TYR E 50 ARG 0.006 0.001 ARG B 210 *********************** 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 163 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8347 (t80) cc_final: 0.7761 (t80) REVERT: A 33 TRP cc_start: 0.6828 (t-100) cc_final: 0.6463 (t-100) REVERT: A 88 GLN cc_start: 0.8573 (pp30) cc_final: 0.7821 (pp30) REVERT: A 191 TYR cc_start: 0.8059 (t80) cc_final: 0.7840 (t80) REVERT: A 274 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8959 (ttmm) REVERT: E 119 ILE cc_start: 0.7452 (mp) cc_final: 0.7088 (pt) REVERT: E 140 ASN cc_start: 0.8694 (m-40) cc_final: 0.8338 (m-40) REVERT: F 49 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7499 (tm-30) REVERT: F 160 LYS cc_start: 0.8798 (tppt) cc_final: 0.7920 (tppt) REVERT: F 161 ASP cc_start: 0.7974 (m-30) cc_final: 0.7773 (m-30) REVERT: C 18 ASP cc_start: 0.8315 (t0) cc_final: 0.8087 (t0) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2120 time to fit residues: 49.1101 Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 216 ASN D 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10585 Z= 0.155 Angle : 0.550 6.370 14405 Z= 0.279 Chirality : 0.041 0.146 1678 Planarity : 0.004 0.048 1808 Dihedral : 4.080 22.706 1446 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.09 % Allowed : 1.76 % Favored : 98.15 % 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: 0.24 (0.23), residues: 1323 helix: 1.81 (0.27), residues: 383 sheet: -0.01 (0.26), residues: 389 loop : -0.85 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 171 HIS 0.004 0.001 HIS B 263 PHE 0.012 0.001 PHE E 141 TYR 0.014 0.001 TYR C 37 ARG 0.005 0.000 ARG C 62 *********************** 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 : 1.195 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8366 (t80) cc_final: 0.7876 (t80) REVERT: A 33 TRP cc_start: 0.6817 (t-100) cc_final: 0.6581 (t-100) REVERT: A 88 GLN cc_start: 0.8555 (pp30) cc_final: 0.8056 (pp30) REVERT: E 119 ILE cc_start: 0.7424 (mp) cc_final: 0.7097 (pt) REVERT: E 140 ASN cc_start: 0.8601 (m-40) cc_final: 0.8250 (m-40) REVERT: F 49 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 50 TRP cc_start: 0.8411 (t60) cc_final: 0.7889 (t60) REVERT: F 160 LYS cc_start: 0.8764 (tppt) cc_final: 0.7823 (tppt) REVERT: F 187 LEU cc_start: 0.8721 (tp) cc_final: 0.8293 (pp) REVERT: C 48 LEU cc_start: 0.9186 (mt) cc_final: 0.8889 (mp) REVERT: C 94 SER cc_start: 0.9050 (m) cc_final: 0.8427 (p) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2174 time to fit residues: 53.2383 Evaluate side-chains 136 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** D 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10585 Z= 0.275 Angle : 0.594 7.126 14405 Z= 0.305 Chirality : 0.043 0.193 1678 Planarity : 0.005 0.079 1808 Dihedral : 4.256 21.860 1446 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % 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: 0.13 (0.23), residues: 1323 helix: 1.64 (0.26), residues: 386 sheet: 0.03 (0.27), residues: 377 loop : -0.95 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 95 HIS 0.007 0.001 HIS A 250 PHE 0.015 0.001 PHE E 141 TYR 0.024 0.001 TYR A 156 ARG 0.009 0.001 ARG D 111 *********************** 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 160 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8372 (t80) cc_final: 0.7892 (t80) REVERT: A 33 TRP cc_start: 0.6904 (t-100) cc_final: 0.6656 (t-100) REVERT: A 88 GLN cc_start: 0.8685 (pp30) cc_final: 0.7938 (pp30) REVERT: E 140 ASN cc_start: 0.8661 (m-40) cc_final: 0.8305 (m-40) REVERT: F 49 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7351 (tm-30) REVERT: F 50 TRP cc_start: 0.8514 (t60) cc_final: 0.8020 (t60) REVERT: F 118 MET cc_start: 0.8573 (mtt) cc_final: 0.8254 (mtt) REVERT: F 160 LYS cc_start: 0.8797 (tppt) cc_final: 0.7904 (tppt) REVERT: F 161 ASP cc_start: 0.7959 (m-30) cc_final: 0.7748 (m-30) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2107 time to fit residues: 47.6683 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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: 0.0060 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10585 Z= 0.178 Angle : 0.569 7.061 14405 Z= 0.290 Chirality : 0.042 0.178 1678 Planarity : 0.004 0.075 1808 Dihedral : 4.136 21.195 1446 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % 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: 0.19 (0.23), residues: 1323 helix: 1.68 (0.26), residues: 384 sheet: 0.05 (0.27), residues: 380 loop : -0.89 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 33 HIS 0.005 0.001 HIS A 250 PHE 0.026 0.001 PHE A 277 TYR 0.011 0.001 TYR C 37 ARG 0.011 0.001 ARG D 111 *********************** 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 : 1.200 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8373 (t80) cc_final: 0.7942 (t80) REVERT: A 88 GLN cc_start: 0.8672 (pp30) cc_final: 0.7798 (pp30) REVERT: E 48 LEU cc_start: 0.9345 (mp) cc_final: 0.9023 (mp) REVERT: E 140 ASN cc_start: 0.8623 (m-40) cc_final: 0.8263 (m-40) REVERT: F 49 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7302 (tm-30) REVERT: F 50 TRP cc_start: 0.8417 (t60) cc_final: 0.7875 (t60) REVERT: F 118 MET cc_start: 0.8385 (mtt) cc_final: 0.8069 (mtt) REVERT: F 160 LYS cc_start: 0.8790 (tppt) cc_final: 0.7846 (tppt) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.2221 time to fit residues: 50.2695 Evaluate side-chains 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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: 0.0970 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 131 ASN F 216 ASN D 42 GLN D 85 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 10585 Z= 0.377 Angle : 0.660 7.780 14405 Z= 0.345 Chirality : 0.044 0.206 1678 Planarity : 0.005 0.073 1808 Dihedral : 4.547 20.474 1446 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 0.18 % Allowed : 0.26 % Favored : 99.56 % 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: 0.02 (0.23), residues: 1323 helix: 1.63 (0.26), residues: 385 sheet: -0.05 (0.26), residues: 378 loop : -1.05 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP E 95 HIS 0.010 0.002 HIS A 250 PHE 0.024 0.002 PHE B 59 TYR 0.018 0.002 TYR E 50 ARG 0.009 0.001 ARG D 111 ********************** 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 160 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8352 (t80) cc_final: 0.7851 (t80) REVERT: A 88 GLN cc_start: 0.8796 (pp30) cc_final: 0.8078 (pp30) REVERT: E 140 ASN cc_start: 0.8771 (m-40) cc_final: 0.8415 (m-40) REVERT: F 50 TRP cc_start: 0.8535 (t60) cc_final: 0.8306 (t60) REVERT: F 160 LYS cc_start: 0.8777 (tppt) cc_final: 0.7897 (tppt) REVERT: F 161 ASP cc_start: 0.8020 (m-30) cc_final: 0.7807 (m-30) REVERT: F 223 LYS cc_start: 0.8509 (mmpt) cc_final: 0.8189 (tppt) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.2045 time to fit residues: 46.9745 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 0.0670 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- 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 131 ASN F 216 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096664 restraints weight = 24765.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094379 restraints weight = 36175.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095839 restraints weight = 26221.513| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3023 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= 0.333 Angle : 0.640 7.852 14405 Z= 0.331 Chirality : 0.044 0.180 1678 Planarity : 0.005 0.079 1808 Dihedral : 4.555 22.916 1446 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.20 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % 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: -0.02 (0.23), residues: 1323 helix: 1.58 (0.26), residues: 385 sheet: -0.15 (0.26), residues: 389 loop : -1.02 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP E 95 HIS 0.008 0.001 HIS A 250 PHE 0.019 0.001 PHE A 277 TYR 0.014 0.001 TYR E 50 ARG 0.007 0.001 ARG E 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.20 seconds wall clock time: 39 minutes 7.04 seconds (2347.04 seconds total)